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Ma J, Zuo D, Zhang X, Li H, Ye H, Zhang N, Li M, Dang M, Geng F, Zhou H, Zhao P. Genome-wide identification analysis of the 4-Coumarate: CoA ligase (4CL) gene family expression profiles in Juglans regia and its wild relatives J. Mandshurica resistance and salt stress. BMC PLANT BIOLOGY 2024; 24:211. [PMID: 38519917 PMCID: PMC10960452 DOI: 10.1186/s12870-024-04899-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
Persian walnut (Juglans regia) and Manchurian walnut (Juglans mandshurica) belong to Juglandaceae, which are vulnerable, temperate deciduous perennial trees with high economical, ecological, and industrial values. 4-Coumarate: CoA ligase (4CL) plays an essential function in plant development, growth, and stress. Walnut production is challenged by diverse stresses, such as salinity, drought, and diseases. However, the characteristics and expression levels of 4CL gene family in Juglans species resistance and under salt stress are unknown. Here, we identified 36 Jr4CL genes and 31 Jm4CL genes, respectively. Based on phylogenetic relationship analysis, all 4CL genes were divided into three branches. WGD was the major duplication mode for 4CLs in two Juglans species. The phylogenic and collinearity analyses showed that the 4CLs were relatively conserved during evolution, but the gene structures varied widely. 4CLs promoter region contained multiply cis-acting elements related to phytohormones and stress responses. We found that Jr4CLs may be participated in the regulation of resistance to anthracnose. The expression level and some physiological of 4CLs were changed significantly after salt treatment. According to qRT-PCR results, positive regulation was found to be the main mode of regulation of 4CL genes after salt stress. Overall, J. mandshurica outperformed J. regia. Therefore, J. mandshurica can be used as a walnut rootstock to improve salt tolerance. Our results provide new understanding the potential functions of 4CL genes in stress tolerance, offer the theoretical genetic basis of walnut varieties adapted to salt stress, and provide an important reference for breeding cultivated walnuts for stress tolerance.
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Affiliation(s)
- Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Dongjun Zuo
- College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Xuedong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Haochen Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Nijing Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Meng Dang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Fangdong Geng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, China.
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China.
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Mackon E, Jeazet Dongho Epse Mackon GC, Yao Y, Guo Y, Ma Y, Dai X, Jandan TH, Liu P. Integrative HPLC profiling and transcriptome analysis revealed insights into anthocyanin accumulation and key genes at three developmental stages of black rice ( Oryza sativa. L) caryopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1211326. [PMID: 37727854 PMCID: PMC10505814 DOI: 10.3389/fpls.2023.1211326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/11/2023] [Indexed: 09/21/2023]
Abstract
Introduction Anthocyanins are plants' secondary metabolites belonging to the flavonoid class with potential health-promoting properties. They are greatly employed in the food industry as natural alternative food colorants for dairy and ready-to-eat desserts and pH indicators. These tremendous advantages make them economically important with increasing market trends. Black rice is a rich source of anthocyanin that can be used to ensure food and nutritional security around the world. However, research on anthocyanin accumulation and gene expression during rice caryopsis development is lacking. Methods In this study, we combined high-performance liquid chromatography (HPLC) and transcriptome analysis to profile the changes in anthocyanin content and gene expression dynamics at three developmental stages (milky, doughy, and mature). Results Our results showed that anthocyanin accumulation started to be visible seven days after flowering (DAF), increased rapidly from milky (11 DAF) to dough stage, then started decreasing after the peak was attained at 18 DAF. RNA-seq showed that 519 out of 14889, 477 out of 17914, and 1614 out of 18810 genes were uniquely expressed in the milky, doughy, and mature stages, respectively. We performed three pairwise comparisons: milky vs. dough, milky vs. mature, and dough vs. mature, and identified 6753, 9540, and 2531 DEGs, respectively. The DEGs' abundance was higher in milky vs. mature, with 5527 up-regulated genes and 4013 down-regulated genes, while it was smaller in dough vs. mature, with 1419 up-regulated genes and 1112 down-regulated DEGs. This result was consistent with the changes in anthocyanin profiling, and the expression of structural, regulatory, and transporter genes involved in anthocyanin biosynthesis showed their highest expression at the dough stage. Through the gene expression profile and protein interaction network, we deciphered six main contributors of the anthocyanin peak observed at dough stage, including OsANS, OsDFR, OsGSTU34, OsMYB3, OsbHLH015, and OsWD40-50. Discussion This study is the first to report the investigation of anthocyanin and gene expression at three developmental stages of black rice caryopsis. The findings of this study could aid in predicting the best harvesting time to achieve maximum anthocyanin content and the best time to collect samples for various gene expression analysis, laying the groundwork for future research into the molecular mechanisms underlying rice caryopsis coloration.
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Affiliation(s)
- Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | | | - Yuhang Yao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yongqiang Guo
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yafei Ma
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xianggui Dai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Tahir Hussain Jandan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Piqing Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
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Ahmad N, Zhang K, Ma J, Yuan M, Zhao S, Wang M, Deng L, Ren L, Gangurde SS, Pan J, Ma C, Li C, Guo B, Wang X, Li A, Zhao C. Transcriptional networks orchestrating red and pink testa color in peanut. BMC PLANT BIOLOGY 2023; 23:44. [PMID: 36658483 PMCID: PMC9850581 DOI: 10.1186/s12870-023-04041-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 01/03/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND Testa color is an important trait of peanut (Arachis hypogaea L.) which is closely related with the nutritional and commercial value. Pink and red are main color of peanut testa. However, the genetic mechanism of testa color regulation in peanut is not fully understood. To elucidate a clear picture of peanut testa regulatory model, samples of pink cultivar (Y9102), red cultivar (ZH12), and two RNA pools (bulk red and bulk pink) constructed from F4 lines of Y9102 x ZH12 were compared through a bulk RNA-seq approach. RESULTS A total of 2992 differential expressed genes (DEGs) were identified among which 317 and 1334 were up-regulated and 225 and 1116 were down-regulated in the bulk red-vs-bulk pink RNA pools and Y9102-vs-ZH12, respectively. KEGG analysis indicates that these genes were divided into significantly enriched metabolic pathways including phenylpropanoid, flavonoid/anthocyanin, isoflavonoid and lignin biosynthetic pathways. Notably, the expression of the anthocyanin upstream regulatory genes PAL, CHS, and CHI was upregulated in pink and red testa peanuts, indicating that their regulation may occur before to the advent of testa pigmentation. However, the differential expression of down-stream regulatory genes including F3H, DFR, and ANS revealed that deepening of testa color not only depends on their gene expression bias, but also linked with FLS inhibition. In addition, the down-regulation of HCT, IFS, HID, 7-IOMT, and I2'H genes provided an alternative mechanism for promoting anthocyanin accumulation via perturbation of lignin and isoflavone pathways. Furthermore, the co-expression module of MYB, bHLH, and WRKY transcription factors also suggested a fascinating transcriptional activation complex, where MYB-bHLH could utilize WRKY as a co-option during the testa color regulation by augmenting anthocyanin biosynthesis in peanut. CONCLUSIONS These findings reveal candidate functional genes and potential strategies for the manipulation of anthocyanin biosynthesis to improve peanut varieties with desirable testa color.
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Affiliation(s)
- Naveed Ahmad
- Institute of crop germplasm resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kun Zhang
- Institute of crop germplasm resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan, 250100, People's Republic of China
| | - Jing Ma
- Institute of crop germplasm resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Mei Yuan
- Shandong Peanut Research Institute, Qingdao, 266199, Shandong, People's Republic of China
| | - Shuzhen Zhao
- Institute of crop germplasm resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Mingqing Wang
- Shandong Peanut Research Institute, Qingdao, 266199, Shandong, People's Republic of China
| | - Li Deng
- Kaifeng Academy of Agriculture and Forestry, Kaifeng, 475008, People's Republic of China
| | - Li Ren
- Kaifeng Academy of Agriculture and Forestry, Kaifeng, 475008, People's Republic of China
| | - Sunil S Gangurde
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA
- Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
| | - Jiaowen Pan
- Institute of crop germplasm resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Changsheng Li
- Institute of crop germplasm resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA
- Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
| | - Xingjun Wang
- Institute of crop germplasm resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Aiqin Li
- Institute of crop germplasm resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
| | - Chuanzhi Zhao
- Institute of crop germplasm resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
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Li C, Shi B, Li X, Zhang W, Pan X. Changes of phenolics contents, antioxidant activities, and enzyme activities in pellicles of Juglans sigillata Dode during fruits development. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2022. [DOI: 10.1080/10942912.2022.2125011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Chunxiang Li
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang China
- College of Agriculture, Guizhou University, Guiyang China
| | - Binbin Shi
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang China
- College of Agriculture, Guizhou University, Guiyang China
| | - Xue Li
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang China
- College of Agriculture, Guizhou University, Guiyang China
| | - Wen’e Zhang
- College of Agriculture, Guizhou University, Guiyang China
| | - Xuejun Pan
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang China
- College of Agriculture, Guizhou University, Guiyang China
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Hou M, Liu S, Yan K, Sun Z, Li S. Downregulation of Odontogenic Ameloblast-associated Protein in the Progression of Periodontal Disease Affects Cell Adhesion, Proliferation, and Migration. Arch Oral Biol 2022; 145:105588. [DOI: 10.1016/j.archoralbio.2022.105588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
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Wang L, Li L, Zhao W, Fan L, Meng H, Zhang G, Wu W, Shi J, Wu G. Integrated metabolomic and transcriptomic analysis of the anthocyanin and proanthocyanidin regulatory networks in red walnut natural hybrid progeny leaves. PeerJ 2022; 10:e14262. [PMID: 36285329 PMCID: PMC9588303 DOI: 10.7717/peerj.14262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/27/2022] [Indexed: 01/24/2023] Open
Abstract
Background Walnuts are among the most important dry fruit crops worldwide, typically exhibiting green leaves and yellow-brown or gray-yellow seed coats. A specific walnut accession with red leaves and seed coats, 'RW-1', was selected for study because of its high anthocyanin and proanthocyanidin (PA) contents. Anthocyanins and PAs are important secondary metabolites and play key roles in plant responses to biotic and abiotic stresses. However, few studies have focused on the molecular mechanism of anthocyanin biosynthesis in walnuts. Methods In this study, we determined the anthocyanin and PA components and their contents in different color leaves of 'RW-1' natural hybrid progenies at various developmental stages. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). We also performed conjoint analyses on DEGs and DAMs to ascertain the degree pathways, and explore the regulation of anthocyanin and PA biosynthesis. Results The results of widely targeted metabolome profiling and anthocyanin detection revealed 395 substances, including four PAs and 26 anthocyanins, in red (SR) and green leaves (SG) of 'RW-1' natural hybrid progenies. From the research, the contents of all anthocyanin components in SR were higher than that in SG. Among them, the contents of delphinidin 3-O-galactoside, cyanidin 3-O-galactoside, delphinidin 3-O-arabinoside and cyanidin 3-O-glucoside were significantly higher than others, and they were considered as the main types of anthocyanins. However, nine anthocyanins were detected only in SR. For PAs, the content of procyanidin C1 was higher in SR compared with SG, while procyanidin B1 and procyanidin B3 were higher in SR-1 and SR-3 but downregulated in SR-2 compared with the controls. Furthermore, transcriptome analysis revealed that the expressions of structural genes (C4H, F3H, F3'5'H, UFGT, LAR and ANR), three MYBs predicted as the activators of anthocyanin and PA biosynthesis, two MYBs predicted as the repressors of anthocyanin biosynthesis, and five WD40s in the anthocyanin and PA biosynthetic pathways were significantly higher in the SR walnuts. Gene-metabolite correlation analyses revealed a core set of 31 genes that were strongly correlated with four anthocyanins and one PA metabolites. The alteration of gene coding sequence altered the binding or regulation of regulatory factors to structural genes in different color leaves, resulting in the effective increase of anthocyanins and PAs accumulation in red walnut. Conclusions This study provides valuable information on anthocyanin and PA metabolites and candidate genes for anthocyanin and PA biosynthesis, yielding new insights into anthocyanin and PA biosynthesis in walnuts.
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Affiliation(s)
- Lei Wang
- Henan Agricultural University, Zhengzhou, China
| | - Lin Li
- Henan Agricultural University, Zhengzhou, China
| | - Wei Zhao
- Henan Agricultural University, Zhengzhou, China
| | - Lu Fan
- Henan Agricultural University, Zhengzhou, China
| | - Haijun Meng
- Henan Agricultural University, Zhengzhou, China
| | | | - Wenjiang Wu
- Henan Agricultural University, Zhengzhou, China
| | - Jiangli Shi
- Henan Agricultural University, Zhengzhou, China
| | - Guoliang Wu
- Henan Agricultural University, Zhengzhou, China
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Wang J, Ye H, Zhou H, Chen P, Liu H, Xi R, Wang G, Hou N, Zhao P. Genome-wide association analysis of 101 accessions dissects the genetic basis of shell thickness for genetic improvement in Persian walnut (Juglans regia L.). BMC PLANT BIOLOGY 2022; 22:436. [PMID: 36096735 PMCID: PMC9469530 DOI: 10.1186/s12870-022-03824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Understanding the underlying genetic mechanisms that drive phenotypic variations is essential for enhancing the efficacy of crop improvement. Persian walnut (Juglans regia L.), which is grown extensively worldwide, is an important economic tree fruit due to its horticultural, medicinal, and material value. The quality of the walnut fruit is related to the selection of traits such as thinner shells, larger filling rates, and better taste, which is very important for breeding in China. The complex quantitative fruit-related traits are influenced by a variety of physiological and environmental factors, which can vary widely between walnut genotypes. RESULTS For this study, a set of 101 Persian walnut accessions were re-sequenced, which generated a total of 906.2 Gb of Illumina sequence data with an average read depth of 13.8× for each accession. We performed the genome-wide association study (GWAS) using 10.9 Mb of high-quality single-nucleotide polymorphisms (SNPs) and 10 agronomic traits to explore the underlying genetic basis of the walnut fruit. Several candidate genes are proposed to be involved in walnut characteristics, including JrPXC1, JrWAKL8, JrGAMYB, and JrFRK1. Specifically, the JrPXC1 gene was confirmed to participate in the regulation of secondary wall cellulose thickening in the walnut shell. CONCLUSION In addition to providing considerable available genetic resources for walnut trees, this study revealed the underlying genetic basis involved in important walnut agronomic traits, particularly shell thickness, as well as providing clues for the improvement of genetic breeding and domestication in other perennial economic crops.
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Affiliation(s)
- Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Ruimin Xi
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Gang Wang
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Na Hou
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
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da Costa Gomes A, Figueiredo CCM, Granero FO, Junior JLB, Ximenes VF, Silva LP, Nicolau-Junior N, da Silva RMG. Antioxidant and antiglycation activities and inhibitory action of Passiflora cincinnata on collagenase, elastase and tyrosinase: in vitro and in silico study. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Zhou T, Sun J, Zhai Y, Gao C, Ruhsam M, Wang X. Transcriptome profiles of yellowish-white and fuchsia colored flowers in the Rheum palmatum complex reveal genes related to color polymorphism. PLANT MOLECULAR BIOLOGY 2022; 110:187-197. [PMID: 35943640 DOI: 10.1007/s11103-022-01299-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Flower color variation is ubiquitous in many plant species, and several studies have been conducted to elucidate the underlying molecular mechanism. There are two flower color variants (yellowish-white and fuchsia) in the Rheum palmatum complex, however, few studies have investigated this phenomenon. Here, we used transcriptome sequencing of the two color variants to shed light on the molecular and biochemical basis for these color morphs. Comparison of the two transcriptomes identified 9641 differentially expressed unigenes (DEGs), including 6477 up-regulated and 3163 down-regulated genes. Functional analyses indicated that several DEGs were related to the anthocyanin biosynthesis pathway, and the expression profiles of these DEGs were coincident with the qRT-PCR validation results, indicating that expression levels of structural genes have a profound effect on the color variation in the R. palmatum complex. Our results suggested that the interaction of transcription factors (MYB, bHLH and WRKY) also regulated the anthocyanin biosynthesis in the R. palmatum complex. Estimation of selection pressures using the dN/dS ratio showed that 1106 pairs of orthologous genes have undergone positive selection. Of these positively selected genes, 21 were involved in the anthocyanin biosynthetic pathway, indicating that they may encode the proteins for structural alteration and affect flower color in the R. palmatum complex.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jiangyan Sun
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yunyan Zhai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenxi Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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Li Y, Zhou Y, Chen H, Chen C, Liu Z, Han C, Wu Q, Yu F. Transcriptomic Analyses Reveal Key Genes Involved in Pigment Biosynthesis Related to Leaf Color Change of Liquidambar formosana Hance. Molecules 2022; 27:molecules27175433. [PMID: 36080201 PMCID: PMC9457658 DOI: 10.3390/molecules27175433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Liquidambar formosana Hance has a highly ornamental value as an important urban greening tree species with bright and beautiful leaf color. To gain insights into the physiological and molecular mechanisms of L. formosana leaf color change, the leaves of three different clones were sampled every ten days from October 13, 2019, five times in total, which are S1, S2, S3, S4 and S5. Transcriptome sequencing was performed at S1 and S4. The chlorophyll content of the three clones decreased significantly, while the anthocyanins content of the three clones increased significantly in the coloring stage. The anthocyanins content of clone 2 was far more than that of the other two clones throughout the period of leaf color change. The transcriptome analysis showed that six DEGs related to anthocyanins biosynthesis, including CHS (chalcone synthase), CHI (chalcone isomerase), F3′H (flavonoid 3′-hydroxylase), DFR (dihydroflavonol 4-reductase), ANS (anthocyanidin synthase) and FLS (flavonol synthase), were found in three clones. Clone 2 has another three DEGs related to anthocyanins biosynthesis, including PAL (Phenylalanine ammonia-lyase), F3′5′H (flavonoid 3′,5′-hydroxylase) and UFGT (flavonoid 3-O-glucosyltransferase). We lay a foundation for understanding the molecular regulation mechanism of the formation of leaf color by exploring valuable genes, which is helpful for L. formosana breeding.
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Affiliation(s)
- Yanjun Li
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Yang Zhou
- Faculty of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Chen Chen
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Zemao Liu
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Chao Han
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
| | - Qikui Wu
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Faculty of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Fangyuan Yu
- Collaborative innovation Centre of Sustainable Forestry in Southern China, Faculty of Forest Science, Nanjing Forestry University, Nanjing 210037, China
- Correspondence:
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11
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Transcriptome analysis of walnut quality formation and color change mechanism of pellicle during walnut development. Gene Expr Patterns 2022; 45:119260. [PMID: 35760355 DOI: 10.1016/j.gep.2022.119260] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 11/21/2022]
Abstract
Walnuts (including those covered with a pellicle) are loved for their rich nutritional value. And the popular varieties of walnut cultivation are Juglans sigillata L. The pellicle (seed coat) of these walnut cultivars has different colors and has an indispensable influence on the walnut quality formation. However, there are few reports on the pellicle color and quality formation in different developmental stages of walnut (Juglans sigillata L.). Therefore, in this study, three walnut cultivars (F, Q, and T) with different pellicle colors were selected for transcriptome sequencing and physiological index analysis of the color and quality formation mechanisms at different development stages. The results showed that with the development of walnut fruit, the starch sucrose metabolism pathway in the pellicle was activated and promoted starch hydrolysis. Meanwhile, the expression levels of genes related to the alpha-linolenic acid metabolism pathway were significantly increased during walnut maturation, especially in F2. Some physiological indicators related to lipid oxidation were also detected and analyzed in this study, such as MDA, CAT, POD and DPPH. These results were similar to the expression patterns of corresponding regulatory genes in the RNA-Seq profile. In addition, lignin synthesis genes were up-regulated in the phenylpropanoid metabolic pathway, while key genes enriched in the flavonoid and anthocyanin synthesis pathways were down-regulated. The results were consistent with the results of total anthocyanins and flavonoid content detection during walnut development. Therefore, this experiment suggested that with the maturation of walnut pellicle, the gene expression in the phenylpropanoid metabolic pathway flowed to the branch of lignin synthesis, especially in the Q variety, resulting in lower flavonoid and anthocyanin content at the maturity stage than immature. This is also the main reason for the pale pellicle of the three walnut varieties after mature. The findings of this study showed that changes in the expression levels of regulating genes for lipid, starch, sugar, and flavonoid synthesis during walnut development influenced the accumulation of the related metabolite for walnut quality formation and pellicle color. The results of this experiment provided the molecular basis and reference for the breeding of high nutritional quality walnut varieties.
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12
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Zhang C, Ren H, Yao X, Wang K, Chang J. Comparative Transcriptome Analysis Reveals Differential Regulation of Flavonoids Biosynthesis Between Kernels of Two Pecan Cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:804968. [PMID: 35283902 PMCID: PMC8914201 DOI: 10.3389/fpls.2022.804968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Flavonoids influence the flavor and nutritional value of pecan nuts. However, limited information is available regarding the molecular mechanisms underlying pecan flavonoid biosynthesis. Here, we used a high ("YLC28") and a low ("Oconee") flavonoid content cultivar as the research objects. The changes in flavonoid content and the gene transcription patterns during kernel development were identified. Different accumulation patterns of total flavonoids (TF) and condensed tannins (CT) were observed between the two cultivars. The contents of TF and CT in "YLC28" were 1.76- and 2.67-fold higher levels than that of "Oconee" on 150 days after full bloom of female flowers, respectively. In total, 30 RNA-Seq libraries were constructed and sequenced. The upregulated genes in "YLC28" were highly enriched in flavonoid-related pathways. Thirty-three structural genes were identified, and the expression of two phenylalanine ammonia lyases, one chalcone synthase, one flavonoid 3',5'-hydroxylase, and one flavonol synthase exhibited high correlation (r ≥ 0.7, p < 0.01) with the condensed tannin content in "YLC28." A putative MYB transcription factor, CIL1093S0100, might act as a flavonoid biosynthesis repressor during kernel development. Altogether, these results will be useful for uncovering the molecular mechanisms of flavonoid biosynthesis and subsequently accelerating quality pecan breeding.
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13
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Liu C, Yang X, Yan Z, Liu D, Feng G. Identification and Characterization of a Mutant PV-PUR Gene Responsible for the Purple Phenotype of Snap Bean ( Phaseolus vulgaris L.). Int J Mol Sci 2022; 23:ijms23031265. [PMID: 35163188 PMCID: PMC8835993 DOI: 10.3390/ijms23031265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
Pod color is a major economic trait of snap beans (Phaseolus vulgaris L.), among which the pod with a purple stripe is more attractive to people. A stable purple mutant with purple stripes on the pods was obtained by artificial mutagenesis with the high generation snap bean inbred line ‘A18-1’. In order to reveal the genetic factors and pathways responsible for the purple appearance in snap bean, we performed transcriptome and metabolome analyses using the green stem and yellow pod cultivar ‘A18-1’ and its purple mutant ‘pv-pur’ via 60Co-γ radiation. Transcriptome analysis showed that three genes in the anthocyanin biosynthetic pathway were differentially expressed, among which the expression level of F3′5′H (Phvul.006G018800) was increased in the mutant ‘pv-pur’, while expression of F3′H (Phvul.004G021200) and ANS (Phvul.002G152700) was downregulated. Anthocyanin-targeted metabonomics analysis showed significant differences in the contents of 10 metabolites between the wild type and mutant plants. Combined analysis of transcriptome and metabolomics showed that one differential metabolite, delphinidin, was related to the differential expression of Phvul.006G024700, Phvul.002G152700, and Phvul.006G018800. Based on the levels of six anthocyanins in wild type and mutant plants, we speculative that the purple appearance of the mutant ‘pv-pur’ is caused by the increased expression of F3′5′H (Phvul.006G018800), the key enzyme in the transformation from dihydroflavanol (DHK) to dihydromyricetone (DHM) in the anthocyanin biosynthetic pathway. The results lay a foundation for further studies on the molecular mechanism of anthocyanin synthesis in snap bean, and provide a framework for breeding different colors of snap bean.
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14
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Zhao W, Liu Y, Li L, Meng H, Yang Y, Dong Z, Wang L, Wu G. Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut ( Juglans regia L.). Front Genet 2021; 12:632509. [PMID: 33719341 PMCID: PMC7943622 DOI: 10.3389/fgene.2021.632509] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/21/2021] [Indexed: 12/31/2022] Open
Abstract
Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut genome and were classified into 15 subfamilies according to sequence similarity and phylogenetic relationships. The gene structure, conserved domains, and chromosome location of the genes were analyzed by bioinformatic methods. Gene duplication analyses revealed that 42 JrbHLHs were involved in the expansion of the walnut bHLH gene family. We also characterized cis-regulatory elements of these genes and performed Gene Ontology enrichment analysis of gene functions, and examined protein-protein interactions. Four candidate genes (JrEGL1a, JrEGL1b, JrbHLHA1, and JrbHLHA2) were found to have high homology to genes encoding bHLH TFs involved in anthocyanin biosynthesis in other plants. RNA sequencing revealed tissue- and developmental stage-specific expression profiles and distinct expression patterns of JrbHLHs according to phenotype (red vs. green leaves) and developmental stage in red walnut hybrid progeny, which were confirmed by quantitative real-time PCR analysis. All four of the candidate JrbHLH proteins localized to the nucleus, consistent with a TF function. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in red walnut.
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Affiliation(s)
- Wei Zhao
- College of Horticulture, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, China
| | - Yonghui Liu
- College of Horticulture, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, China
| | - Lin Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, China
| | - Haijun Meng
- College of Horticulture, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, China
| | - Ying Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, China
| | - Zhaobin Dong
- Shangluo Shengda Industrial Co., Ltd., Luonan, China
| | - Lei Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, China
| | - Guoliang Wu
- College of Horticulture, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou, China
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15
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Zou S, Shahid MQ, Zhao C, Wang M, Bai Y, He Y, Lin S, Yang X. Transcriptional analysis for the difference in carotenoids accumulation in flesh and peel of white-fleshed loquat fruit. PLoS One 2020; 15:e0233631. [PMID: 32589636 PMCID: PMC7319346 DOI: 10.1371/journal.pone.0233631] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/08/2020] [Indexed: 11/30/2022] Open
Abstract
Loquat (Eriobotrya japonica Lindl.) is divided into yellow- and white-fleshed based on the difference in fruit color, and the variations in carotenoids accumulation are considered as the main reasons for this difference. Using RNA-seq technology, a transcriptome analysis was carried out on the flesh and peel of ‘Baiyu’ fruit during four different fruit development stages. A total of 172.53 Gb clean reads with an average of 6.33 Gb reads were detected for each library, and the percentage of Q30 was higher than 90.84%. We identified 16 carotenogenic and 13 plastid-lipid-associated protein (PAP) genes through RNA-seq. Of these, five carotenogenic and four PAP related genes exhibited remarkable differences in the expression patterns. Carotenoids biosynthetic genes, including DXS, PSY1 and VDE displayed higher expression levels in peel than that in the flesh. However, carotenoids decomposition gene, such as NCDE1, exhibited higher expression in flesh than that in the peel. Notably, all differentially expressed PAP genes showed higher expression levels in peel than flesh. We inferred that the differential accumulation of carotenoids in flesh and peel of 'Baiyu' is caused by the up- or down-regulation of the carotenogenic and PAP related genes. The functional analysis of these important genes will provide valuable information about underlying molecular mechanism of carotenoids accumulation in loquat.
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Affiliation(s)
- Shicheng Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Tianhe District, Guangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Tianhe District, Guangzhou, China
| | - Chongbin Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Tianhe District, Guangzhou, China
| | - Man Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Tianhe District, Guangzhou, China
| | - Yunlu Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Tianhe District, Guangzhou, China
| | - Yehua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Tianhe District, Guangzhou, China
| | - Shunquan Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Tianhe District, Guangzhou, China
- * E-mail: (YXH); (LSQ)
| | - Xianghui Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Tianhe District, Guangzhou, China
- * E-mail: (YXH); (LSQ)
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16
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Vangelisti A, Guidi L, Cavallini A, Natali L, Lo Piccolo E, Landi M, Lorenzini G, Malorgio F, Massai R, Nali C, Pellegrini E, Rallo G, Remorini D, Vernieri P, Giordani T. Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes. Sci Rep 2020; 10:1959. [PMID: 32029804 PMCID: PMC7005320 DOI: 10.1038/s41598-020-58878-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/02/2020] [Indexed: 11/08/2022] Open
Abstract
The final stage of leaf ontogenesis is represented by senescence, a highly regulated process driven by a sequential cellular breakdown involving, as the first step, chloroplast dismantling with consequent reduction of photosynthetic efficiency. Different processes, such as pigment accumulation, could protect the vulnerable photosynthetic apparatus of senescent leaves. Although several studies have produced transcriptomic data on foliar senescence, just few works have attempted to explain differences in red and green leaves throughout ontogenesis. In this work, a transcriptomic approach was used on green and red leaves of Prunus cerasifera to unveil molecular differences from leaf maturity to senescence. Our analysis revealed a higher gene regulation in red leaves compared to green ones, during leaf transition. Most of the observed DEGs were shared and involved in transcription factor activities, senescing processes and cell wall remodelling. Significant differences were detected in cellular functions: genes related to photosystem I and II were highly down-regulated in the green genotype, whereas transcripts involved in flavonoid biosynthesis, such as UDP glucose-flavonoid-3-O-glucosyltransferase (UFGT) were exclusively up-regulated in red leaves. In addition, cellular functions involved in stress response (glutathione-S-transferase, Pathogen-Related) and sugar metabolism, such as three threalose-6-phosphate synthases, were activated in senescent red leaves. In conclusion, data suggests that P. cerasifera red genotypes can regulate a set of genes and molecular mechanisms that cope with senescence, promoting more advantages during leaf ontogenesis than compared to the green ones.
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Affiliation(s)
- Alberto Vangelisti
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Lucia Guidi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
- CIRSEC, Centre for Climate Change Impact, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Lucia Natali
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
- CIRSEC, Centre for Climate Change Impact, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Ermes Lo Piccolo
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Landi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
- CIRSEC, Centre for Climate Change Impact, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Giacomo Lorenzini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
- CIRSEC, Centre for Climate Change Impact, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Fernando Malorgio
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Rossano Massai
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Cristina Nali
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
- CIRSEC, Centre for Climate Change Impact, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Elisa Pellegrini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
- CIRSEC, Centre for Climate Change Impact, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Giovanni Rallo
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
- CIRSEC, Centre for Climate Change Impact, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Damiano Remorini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
- CIRSEC, Centre for Climate Change Impact, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Paolo Vernieri
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
- CIRSEC, Centre for Climate Change Impact, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
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17
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Xia H, Zhu L, Zhao C, Li K, Shang C, Hou L, Wang M, Shi J, Fan S, Wang X. Comparative transcriptome analysis of anthocyanin synthesis in black and pink peanut. PLANT SIGNALING & BEHAVIOR 2020; 15:1721044. [PMID: 32009540 PMCID: PMC7053958 DOI: 10.1080/15592324.2020.1721044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 06/01/2023]
Abstract
In recent years, black testa peanut (Arachis hypogaea L.) has been favored because of its nutritional value and health function. To explore the genetic basis of peanut testa color, high-throughput sequencing technology was used to sequence the transcriptome of black testa peanut 'ZH9' and pink testa peanut 'ZH8.' Over 18 million high-quality reads were assembled into 49,404-52,578 genes for these two cultivars using a combined assembly strategy. Totally, 4,122 differentially expressed genes (DEGs) were identified between ZH8 and ZH9, among which 1317 (32%) were up-regulated and 2805 (68%) were down-regulated. KEGG analysis showed that the pathways of anthocyanin biosynthesis, isoflavonoid biosynthesis, flavone and flavonol biosynthesis, and phenylpropanoid biosynthesis were in the top 20 differentially expressed genes enriched pathways. Further analysis showed that the formation of the black color of ZH9 testa was mainly due to the reduction of lignin biosynthesis and isoflavonoid biosynthesis, and as a result, more substrate flow to anthocyanin biosynthesis. The up-regulation of all genes associated with DFR, a key enzyme determining flavonoid synthesis or anthocyanin synthesis in the flavonoid metabolic pathway, is also a strategy for increasing dihydroflavonol, a substrate for anthocyanin and flavonol biosynthesis. In addition, we identified three up-regulated R2R3MYB transcription factors associated with anthocyanin biosynthesis in ZH9. Finally, we verified the expressions of 15 genes that encode key enzymes and transcription factors using quantitative real-time PCR (qRT-PCR).
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Affiliation(s)
- Han Xia
- College of Life Sciences, Shandong Normal University, Ji’nan, China
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji’nan, China
| | - Lin Zhu
- College of Life Sciences, Shandong Normal University, Ji’nan, China
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji’nan, China
| | - Chuanzhi Zhao
- College of Life Sciences, Shandong Normal University, Ji’nan, China
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji’nan, China
| | - Ke Li
- College of Life Sciences, Shandong Normal University, Ji’nan, China
| | - Caili Shang
- College of Life Sciences, Shandong Normal University, Ji’nan, China
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji’nan, China
| | - Lei Hou
- College of Life Sciences, Shandong Normal University, Ji’nan, China
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji’nan, China
| | - Mingxiao Wang
- College of Life Sciences, Shandong Normal University, Ji’nan, China
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji’nan, China
| | - Jing Shi
- College of Life Sciences, Shandong Normal University, Ji’nan, China
| | - Shoujin Fan
- College of Life Sciences, Shandong Normal University, Ji’nan, China
| | - Xingjun Wang
- College of Life Sciences, Shandong Normal University, Ji’nan, China
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Ji’nan, China
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18
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Wang D, Cao D, Yao Y, Wang J, Li Z, Liu B. Understanding the chemical foundation and genetic mechanism of the black grain trait in quinoa by integrating metabolome and transcriptome analyses. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1822207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Dongxia Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Dong Cao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, People’s Republic of China
- Laboratory of Wheat Quality Improvement, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, Qinghai, People’s Republic of China
| | - Youhua Yao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Jinmin Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Zongren Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, People’s Republic of China
| | - Baolong Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, People’s Republic of China
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, People’s Republic of China
- Laboratory of Wheat Quality Improvement, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, Qinghai, People’s Republic of China
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19
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Functional Components, Antioxidant Activity and Hypoglycemic Ability Following Simulated Gastro-Intestinal Digestion of Pigments from Walnut Brown Shell and Green Husk. Antioxidants (Basel) 2019; 8:antiox8120573. [PMID: 31766437 PMCID: PMC6943620 DOI: 10.3390/antiox8120573] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/13/2019] [Accepted: 11/20/2019] [Indexed: 12/05/2022] Open
Abstract
To assess the effects of digestion on the functional components of walnut pigment and their bioactivities, we developed an in vitro model simulating gastro-intestinal digestion. Results showed an increase in the contents of flavonoids and conjugated phenols (with retention rates higher than 100%) in husk pigment after digestion. The lowest of the 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging abilities was reached in the group with the minimum flavonoid content after digestion. Close correlation was observed between free phenol content and total reducing power, as the reducing power among different groups of husk pigment was in consistent with free phenols changes. The inhibitory effect of walnut pigment on α-amylase with/without digestion enzyme was similar. However, shell pigment showed improved inhibitory effect on α-glucosidase activity, with an increased inhibitory rate of 5.42%. In general, the antioxidant activity and hypoglycemic ability of walnut pigment were prone to chemical and enzymatic changes during simulated digestion, which were also related to the alteration of flavonoids and phenols.
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20
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Luo X, Liu J. Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut. Genes (Basel) 2019; 10:E605. [PMID: 31405132 PMCID: PMC6723594 DOI: 10.3390/genes10080605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
We reported changes in the co-regulated mRNA expression in iron walnut (Juglans sigillata) in response to soil pH treatments and identified mRNAs specific to acidic soil conditions. Phenotypic and physiological analyses revealed that iron walnut growth was greater for the pH 4-5 and pH 5-6 treatments than for the pH 3-4 and pH 6-7 treatments. A total of 2768 differentially expressed genes were detected and categorized into 12 clusters by Short Time-series Expression Miner (STEM). The 994 low-expression genes in cluster III and 255 high-expression genes in cluster X were classified as acid-responsive genes on the basis of the relationships between phenotype, physiology, and STEM clustering, and the two gene clusters were analyzed by a maximum likelihood (ML) evolutionary tree with the greatest log likelihood values. No prominent sub-clusters occurred in cluster III, but three occurred in cluster X. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that acid-responsive genes were related primarily to arginine biosynthesis and the arginine/proline metabolism pathway, implying that polyamine accumulation may enhance iron walnut acid stress tolerance. Overall, our results revealed 1249 potentially acid-responsive genes in iron walnut, indicating that its response to acid stress involves different pathways and activated genes.
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Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Huimin Road 211 in Wenjiang District, Chengdu 611130, China.
| | - Juncheng Liu
- College of Forestry, Sichuan Agricultural University, Huimin Road 211 in Wenjiang District, Chengdu 611130, China
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21
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Zuo J, Wang Y, Zhu B, Luo Y, Wang Q, Gao L. Network analysis of noncoding RNAs in pepper provides insights into fruit ripening control. Sci Rep 2019; 9:8734. [PMID: 31217463 PMCID: PMC6584694 DOI: 10.1038/s41598-019-45427-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/06/2019] [Indexed: 01/21/2023] Open
Abstract
Pepper is an important vegetable worldwide and is a model plant for nonclimacteric fleshy fruit ripening. Drastic visual changes and internal biochemical alterations are involved in fruit coloration, flavor, texture, aroma, and palatability to animals during the pepper fruit ripening process. To explore the regulation of bell pepper fruit ripening by noncoding RNAs (ncRNAs), we examined their expression profiles; 43 microRNAs (miRNAs), 125 circular RNAs (circRNAs), 366 long noncoding RNAs (lncRNAs), and 3266 messenger RNAs (mRNAs) were differentially expressed (DE) in mature green and red ripe fruit. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the targets of the DE ncRNAs and DE mRNAs included several kinds of transcription factors (TFs) (ERF, bHLH, WRKY, MYB, NAC, bZIP, and ARF), enzymes involved in cell wall metabolism (beta-galactosidase, beta-glucosidase, beta-amylase, chitinase, pectate lyase (PL), pectinesterase (PE) and polygalacturonase (PG)), enzymes involved in fruit color accumulation (bifunctional 15-cis-phytoene synthase, 9-cis-epoxycarotenoid dioxygenase, beta-carotene hydroxylase and carotene epsilon-monooxygenase), enzymes associated with fruit flavor and aroma (glutamate-1-semialdehyde 2,1-aminomutase, anthocyanin 5-aromatic acyltransferase, and eugenol synthase 1) and enzymes involved in the production of ethylene (ET) (ACO1/ACO4) as well as other plant hormones such as abscisic acid (ABA), auxin (IAA), and gibberellic acid (GA). Based on accumulation profiles, a network of ncRNAs and mRNAs associated with bell pepper fruit ripening was developed that provides a foundation for further developing a more refined understanding of the molecular biology of fruit ripening.
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Affiliation(s)
- Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing, Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China. .,Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, 14853, USA.
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing, Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing, Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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22
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Fang Z, Hou Z, Wang S, Liu Z, Wei S, Zhang Y, Song J, Yin J. Transcriptome Analysis Reveals the Accumulation Mechanism of Anthocyanins in Buckwheat ( Fagopyrum esculentum Moench) Cotyledons and Flowers. Int J Mol Sci 2019; 20:E1493. [PMID: 30934615 PMCID: PMC6471586 DOI: 10.3390/ijms20061493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/20/2019] [Accepted: 03/23/2019] [Indexed: 12/20/2022] Open
Abstract
Buckwheat (Fagopyrum esculentum) is a valuable crop which can produce multiple human beneficial secondary metabolites, for example, the anthocyanins in sprouts and flowers. However, as the predominant group of visible polyphenols in pigmentation, little is known about the molecular mechanisms underlying the anthocyanin biosynthesis within buckwheat. In this study, a comparative transcriptome analysis of green and red common buckwheat cultivars was carried out through RNA sequencing. Overall, 3727 and 5323 differently expressed genes (DEGs) were identified in flowers and cotyledons, respectively. Through GO and KEGG analysis, we revealed that DEGs in flowers and cotyledons are predominately involved in biosynthesis of anthocyanin. A total of 42 unigenes encoding 11 structural enzymes of the anthocyanin biosynthesis were identified as DEGs. We also identified some transcription factor families involved in the regulation of anthocyanin biosynthesis. Real-time qPCR validation of candidate genes was performed in flowers and cotyledons, and the results suggested that the high expression level of structural genes involved in anthocyanin biosynthetic pathway promotes anthocyanin accumulation. Our results provide the insight understanding for coloration of red common buckwheat.
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Affiliation(s)
- Zhengwu Fang
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Zehao Hou
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Shuping Wang
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Zhixiong Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434000, China.
| | - Shudong Wei
- College of Life Science, Yangtze University, Jingzhou 434000, China.
| | - Yingxin Zhang
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Jinghan Song
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Junliang Yin
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
- Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/Engendering Research Center of Ecology and Agricultural Use of Waterland, Ministry of Education, Yangtze University, Jingzhou 434000, China.
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23
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Cao D, Fan J, Xi X, Zong Y, Wang D, Zhang H, Liu B. Transcriptome Analysis Identifies Key Genes Responsible for Red Coleoptiles in Triticum Monococcum. MOLECULES (BASEL, SWITZERLAND) 2019; 24:molecules24050932. [PMID: 30866466 PMCID: PMC6429503 DOI: 10.3390/molecules24050932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 11/16/2022]
Abstract
Red coleoptiles can help crops to cope with adversity and the key genes that are responsible for this trait have previously been isolated from Triticum aestivum, Triticum urartu, and Aegilops tauschii. This report describes the use of transcriptome analysis to determine the candidate gene that controls the trait for white coleoptiles in T. monococcum by screening three cultivars with white coleoptiles and two with red coleoptiles. Fifteen structural genes and two transcription factors that are involved in anthocyanin biosynthesis were identified from the assembled UniGene database through BLAST analysis and their transcript levels were then compared in white and red coleoptiles. The majority of the structural genes reflected lower transcript levels in the white than in the red coleoptiles, which implied that transcription factors related to anthocyanin biosynthesis could be candidate genes. The transcript levels of MYC transcription factor TmMYC-A1 were not significantly different between the white and red coleoptiles and all of the TmMYC-A1s contained complete functional domains. The deduced amino acid sequence of the MYB transcription factor TmMYB-A1 in red coleoptiles was homologous to TuMYB-A1, TaMYB-A1, TaMYB-B1, and TaMYB-D1, which control coleoptile color in corresponding species and contained the complete R2R3 MYB domain and the transactivation domain. TmMYB-a1 lost its two functional domains in white coleoptiles due to a single nucleotide deletion that caused premature termination at 13 bp after the initiation codon. Therefore, TmMYB-A1 is likely to be the candidate gene for the control of the red coleoptile trait, and its loss-of-function mutation leads to the white phenotype in T. monococcum.
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Affiliation(s)
- Dong Cao
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, Qinghai, China.
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 800010, Qinghai, China.
| | - Jiequn Fan
- Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Xingyuan Xi
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, Qinghai, China.
| | - Yuan Zong
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 800010, Qinghai, China.
| | - Dongxia Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 800010, Qinghai, China.
| | - Huaigang Zhang
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, Qinghai, China.
| | - Baolong Liu
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining 810008, Qinghai, China.
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24
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Zhang C, Yao X, Ren H, Chang J, Wang K. RNA-Seq Reveals Flavonoid Biosynthesis-Related Genes in Pecan ( Carya illinoinensis) Kernels. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:148-158. [PMID: 30563335 DOI: 10.1021/acs.jafc.8b05239] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pecan ( Carya illinoinensis) is an important tree nut throughout the world. The high concentration of flavonoid in its kernels makes it an excellent food with health benefits. However, the molecular basis of flavonoid biosynthesis in pecan remains unclear, which hinders quality breeding in this plant. Therefore, in order to find the crucial genes involved in flavonoid biosynthesis, the changes in flavonoid profiles and the transcriptomes of pecan kernels at four developmental stages (late water, gel, dough, and mature stages) were analyzed. As a result, the highest levels of total phenolic, condensed tannin, and flavan-3-ols were observed at the "late water stage". Catechin was the most abundant flavan-3-ol at different development stages. In total, 64 773 unigenes were obtained, and 46 924 (72.44%) unigenes were annotated. After differentially expressed gene (DEG) analysis, 12 750 unique DEGs were identified. Flavonoid-related DEGs of 36 structural genes and eight MYBs were obtained. The structural gene set contained three PALs, three CHSs, two CHIs, one F3H, two F3'Hs, two F3'5'Hs, one DFR, one ANS, two LARs, and two ANRs. The expression patterns of most of the structural genes were consistent with the changes in flavonoid profiles during kernel development. We believe that this RNA-Seq data set will provide valuable resources for unraveling the molecular mechanism of flavonoid metabolism in pecan and will significantly promote genetic studies and quality breeding in this plant.
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Affiliation(s)
- Chengcai Zhang
- Research Institute of Subtropical Forestry , Chinese Academy of Forestry , Fuyang District, Hangzhou , Zhejiang Province 311400 , China
| | - Xiaohua Yao
- Research Institute of Subtropical Forestry , Chinese Academy of Forestry , Fuyang District, Hangzhou , Zhejiang Province 311400 , China
| | - Huadong Ren
- Research Institute of Subtropical Forestry , Chinese Academy of Forestry , Fuyang District, Hangzhou , Zhejiang Province 311400 , China
| | - Jun Chang
- Research Institute of Subtropical Forestry , Chinese Academy of Forestry , Fuyang District, Hangzhou , Zhejiang Province 311400 , China
| | - Kailiang Wang
- Research Institute of Subtropical Forestry , Chinese Academy of Forestry , Fuyang District, Hangzhou , Zhejiang Province 311400 , China
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25
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Hou X, Guo Q, Wei W, Guo L, Guo D, Zhang L. Screening of Genes Related to Early and Late Flowering in Tree Peony Based on Bulked Segregant RNA Sequencing and Verification by Quantitative Real-Time PCR. Molecules 2018; 23:molecules23030689. [PMID: 29562683 PMCID: PMC6017042 DOI: 10.3390/molecules23030689] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/10/2018] [Accepted: 03/12/2018] [Indexed: 01/13/2023] Open
Abstract
Tree peony (Paeonia suffruticosa Andrews) is a perennial woody shrub bearing large and colorful flowers. However, the flowering period is short and relatively uniform, which to an important extent hinders the cultivation and exploitation of ornamental peonies. In this study, the segregation of an F1 population derived from P. ostti ‘Feng Dan’ (an early-flowering cultivar) × P. suffruticosa ‘Xin Riyuejin’ (a late-flowering cultivar) was used to screen and analyze candidate genes associated with flowering period of the two parents. Extreme early- and late-flowering genotypes of the F1 population at full-bloom stage were sampled to establish an early-flowering mixed pool (T03), a late-flowering mixed pool (T04), a late-flowering male pool (T01), and an early-flowering female pool (T02), using the Sequencing By Synthesis (SBS) technology on the Illumina HiSeq TM2500 platform. A total of 56.51 Gb of clean reads data, comprising at least 87.62% of Quality30 (Q30), was generated, which was then combined into 173,960 transcripts (N50 = 1781) and 78,645 (N50 = 1282) unigenes, with a mean length of 1106.76 and 732.27 base pairs (bp), respectively. Altogether, 58,084 genes were annotated by comparison with public databases, based on an E-value parameter of less than 10−5 and 10−10 for BLAST and HMMER, respectively. In total, 291 unigene sequences were finally screened out by BSR-seq (bulked segregant RNA-seq) association analysis. To validate these unigenes, we finally confirmed seven unigenes that were related to early and late flowering, which were then verified by quantitative real-time PCR (qRT-PCR). This is the first reported study to screen genes associated with early and late flowering of tree peony by the BSA (bulked sample analysis) method of transcriptome sequencing, and to construct a high-quality transcriptome database. A set of candidate functional genes related to flowering time was successfully obtained, providing an important genetic resource for further studies of flowering in peony and the mechanism of regulation of flowering time in tree peony.
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Affiliation(s)
- Xiaogai Hou
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
| | - Qi Guo
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Weiqiang Wei
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
| | - Lili Guo
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
| | - Dalong Guo
- College of Forestry, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
| | - Lin Zhang
- College of Agriculture, Henan University of Science & Technology, 263 Kaiyuan Avenue, Luoyang 471023, China.
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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