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Chen J, Tao F, Xue Y, Xu B, Li X. Genome-Wide Identification of the WRKY Gene Family and Functional Characterization of CpWRKY5 in Cucurbita pepo. Int J Mol Sci 2024; 25:4177. [PMID: 38673762 PMCID: PMC11049939 DOI: 10.3390/ijms25084177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/27/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The WRKY gene family is crucial for regulating plant growth and development. However, the WRKY gene is rarely studied in naked kernel formation in hull-less Cucurbita pepo L. (HLCP), a natural mutant that lacks the seed coat. In this research, 76 WRKY genes were identified through bioinformatics-based methods in C. pepo, and their phylogenetics, conserved motifs, synteny, collinearity, and temporal expression during seed coat development were analyzed. The results showed that 76 CpWRKYs were identified and categorized into three main groups (I-III), with Group II further divided into five subgroups (IIa-IIe). Moreover, 31 segmental duplication events were identified in 49 CpWRKY genes. A synteny analysis revealed that C. pepo shared more collinear regions with cucumber than with melon. Furthermore, quantitative RT-PCR (qRT-PCR) results indicated the differential expression of CpWRKYs across different varieties, with notable variations in seed coat development between HLCP and CP being attributed to differences in CpWRKY5 expression. To investigate this further, CpWRKY5-overexpression tobacco plants were generated, resulting in increased lignin content and an upregulation of related genes, as confirmed by qRT-PCR. This study offers valuable insights for future functional investigations of CpWRKY genes and presents novel information for understanding the regulation mechanism of lignin synthesis.
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Affiliation(s)
- Junhong Chen
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Fei Tao
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Yingyu Xue
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Bingliang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaowei Li
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (J.C.); (F.T.); (X.L.)
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
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Yazıcı K, Gönülkırmaz B, Şahin Çevik M. Development of Molecular Marker Linked to Seed Hardness in Pomegranate Using Bulked Segregant Analysis. Life (Basel) 2023; 13:life13051123. [PMID: 37240768 DOI: 10.3390/life13051123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
The pomegranate (Punica granatum L.) is one of the fruit species with the oldest cultural history. There are many traits to determine the quality of pomegranate fruits. Among them, soft-seeded feature of pomegranate fruit is important trait for the market value of the fruit. For this reason, the demand for pomegranate varieties with soft seeds has been increasing, especially in recent years. In this study, molecular markers associated with seed hardness were developed to distinguish pomegranate cultivars with soft-seeded feature based on genomic DNA at the early stages of the pomegranate breeding process. For this purpose, pomegranate genotypes and/or cultivars from the population involved in reciprocal crosses of hard-seeded Ernar, medium-hard-seeded Hicaznar, and soft-seeded Fellahyemez cultivars were grouped as soft-seeded or hard-seeded. Further, leaf samples were collected from individuals belonging to each group. Then, the genomic DNA was isolated from each plant separately, and equal amount of genomic DNA from individuals with the similar seed hardness were mixed for bulked segregant analysis (BSA). The bulked genomic DNAs of opposite characters were analyzed by polymerase chain reaction (PCR) using random decamer primers to develop random amplified polymorphic DNA (RAPD) markers associated with soft-seeded or hard-seeded pomegranates. A total of three RAPD markers were determined to distinguish the individuals having soft- or hard-seeded pomegranate genotypes and/or cultivars. As a result of the comparison of the DNA sequences of these RAPD markers, insertion-deletions (inDels) primers were designed to developed and validate a PCR assay to distinguish the soft- and hard-seeded pomegranate genotypes/cultivars from each other. The molecular markers developed in this study will enable us to distinguish soft-seeded pomegranate types easily in a short time at the early stages of the pomegranate breeding programs.
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Affiliation(s)
- Keziban Yazıcı
- Department of Horticultural Sciences, Faculty of Agriculture, Recep Tayyip Erdoğan University, Rize 53300, Turkey
| | - Betül Gönülkırmaz
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ispara University of Applied Sciences, Isparta 32260, Turkey
| | - Mehtap Şahin Çevik
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ispara University of Applied Sciences, Isparta 32260, Turkey
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Bai Y, Ali S, Liu S, Zhou J, Tang Y. Characterization of plant laccase genes and their functions. Gene 2023; 852:147060. [PMID: 36423777 DOI: 10.1016/j.gene.2022.147060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Laccase is a copper-containing polyphenol oxidase found in different organisms. The multigene family that encodes laccases is widely distributed in plant genomes. Plant laccases oxidize monolignols to produce lignin which is important for plant growth and stress responses. Industrial applications of fungal and bacterial laccases are extensively explored and addressed. Recently many studies have focused on the significance of plant laccase, particularly in crop yield, and its functions in different environmental conditions. This review summarizes the transcriptional and posttranscriptional regulation of plant laccase genes and their functions in plant growth and development. It especially describes the responses of laccase genes to various stresses and their contributions to plant biotic and abiotic stress resistance. In-depth explanations and scientific advances will serve as foundations for research into plant laccase genes' function, mechanism, and possible applications.
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Affiliation(s)
- Yongsheng Bai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong, PR China
| | - Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong, PR China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Shuai Liu
- Shaanxi Academy of Traditional Chinese Medicine, Xi'an, Shaanxi 710003, China
| | - Jiajie Zhou
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong, PR China
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, Guangdong, PR China.
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Identification and Functional Analysis of CAD Gene Family in Pomegranate ( Punica granatum). Genes (Basel) 2022; 14:genes14010026. [PMID: 36672766 PMCID: PMC9858471 DOI: 10.3390/genes14010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
[Objective] Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. The aim of this study was to identify CAD gene family members in pomegranate and its expression correlation with seed hardness. [Methods] Based on the reported CAD sequence of Arabidopsis, the CAD gene family of pomegranate was identified by homologous comparison, and then phylogenetic, molecular characterization, and expression profile analysis were performed. [Results] Pomegranate CAD gene family has 25 members, distributed on seven chromosomes of pomegranate. All pomegranate CAD proteins have similar physical and chemical properties. We divide the family into four groups based on evolutionary relationships. The member of group I, called bona fide CAD, was involved in lignin synthesis. Most of the members of group II were involved in stress resistance. The functions of groups III and IV need to be explored. We found four duplicated modes (whole genome duplication or segmental (WGD), tandem duplication (TD), dispersed duplication (DSD), proximal duplication (PD) in this family; TD (36%) had the largest number of them. We predicted that 20 cis-acting elements were involved in lignin synthesis, stress resistance, and response to various hormones. Gene expression profiles further demonstrated that the PgCAD gene family had multiple functions. [Conclusions] Pomegranate CAD gene family is involved in lignin synthesis of hard-seeded cultivar Hongyushizi and Baiyushizi, but its role in seed hardness of soft-seeded cultivar Tunisia needs to be further studied.
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Feng L, Wang C, Yang X, Jiao Q, Yin Y. Transcriptomics and metabolomics analyses identified key genes associated with sugar and acid metabolism in sweet and sour pomegranate cultivars during the developmental period. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 181:12-22. [PMID: 35421745 DOI: 10.1016/j.plaphy.2022.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Pomegranate (Punica granatum), an important fruit tree in the world, is rich in bioactive substances and has broad prospects for development. In this study, gene expression levels and the concentrations of metabolites involved in the metabolism of soluble sugars and organic acids were investigated in sweet and sour pomegranate cultivars at the S1 (July 25) stage, S2 (August 26) stage, and S3 (September 24) stage. The results showed that glucose, fructose, citric acid, and malic acid were predominantly present in pomegranate. The expression of invertase 2 (INV2), INV1, FRK2, FRK7, PFK2, PFK7, and HK1 was closely correlated with the fructose and glucose contents during different developmental stages, whereas the expression of sucrose synthase 3 (SUS3) and INV1 was negatively correlated with the sucrose content. The expression of MDH (c28468_g3) and WRKY42 (c20711_g1) genes were closely related to the content of sucrose, malic acid, citric acid, and succinic acid during different developmental stages. Gene expression and metabolite concentrations varied between the two cultivars. The results provide valuable information for gene discovery, marker-assisted selection, and investigation of metabolism mechanisms in pomegranate fruits.
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Affiliation(s)
- Lijuan Feng
- Shandong Institute of Pomology, 66 Longtan Rd., Tai'an, 271000, China.
| | - Chuanzeng Wang
- Shandong Academy of Agricultural Sciences, 202Gongye North Rd., Jinan, 250100, China
| | - Xuemei Yang
- Shandong Institute of Pomology, 66 Longtan Rd., Tai'an, 271000, China
| | - Qiqing Jiao
- Shandong Academy of Agricultural Sciences, 202Gongye North Rd., Jinan, 250100, China
| | - Yanlei Yin
- Shandong Institute of Pomology, 66 Longtan Rd., Tai'an, 271000, China
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Patil PG, Singh NV, Bohra A, Jamma S, N M, C VS, Karuppannan DB, Sharma J, Marathe RA. Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.). Front Genet 2022; 13:866504. [PMID: 35495126 PMCID: PMC9040167 DOI: 10.3389/fgene.2022.866504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Present research discovered novel miRNA-SSRs for seed type trait from 761 potential precursor miRNA sequences of pomegranate. SSR mining and BLASTx of the unique sequences identified 69 non-coding pre-miRNA sequences, which were then searched for BLASTn homology against Dabenzi genome. Sixty three true pri-miRNA contigs encoding 213 pre-miRNAs were predicted. Analysis of the resulting sequences enabled discovery of SSRs within pri-miRNA (227) and pre-miRNA sequences (79). A total of 132 miRNA-SSRs were developed for seed type trait from 63 true pri-miRNAs, of which 46 were specific to pre-miRNAs. Through ePCR, 123 primers were validated and mapped on eight Tunisia chromosomes. Further, 80 SSRs producing specific amplicons were ePCR-confirmed on multiple genomes i.e. Dabenzi, Taishanhong, AG2017 and Tunisia, yielding a set of 63 polymorphic SSRs (polymorphism information content ≥0.5). Of these, 32 miRNA-SSRs revealed higher polymorphism level (89.29%) when assayed on six pomegranate genotypes. Furthermore, target prediction and network analysis suggested a possible association of miRNA-SSRs i.e. miRNA_SH_SSR69, miRNA_SH_SSR36, miRNA_SH_SSR103, miRNA_SH_SSR35 and miRNA_SH_SSR53 with seed type trait. These miRNA-SSRs would serve as important genomic resource for rapid and targeted improvement of seed type trait of pomegranate.
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Affiliation(s)
- Prakash Goudappa Patil
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
- *Correspondence: Prakash Goudappa Patil,
| | | | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Shivani Jamma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Manjunatha N
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Venkatesh S. C
- Dept. of Biotechnology and Crop Improvement, University of Horticultural Sciences (UHS), Bagalkot, India
| | | | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Rajiv A. Marathe
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
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Xue Y, Shen Z, Tao F, Zhou J, Xu B. Transcriptomic Analysis Reveal the Molecular Mechanisms of Seed Coat Development in Cucurbita pepo L. FRONTIERS IN PLANT SCIENCE 2022; 13:772685. [PMID: 35283914 PMCID: PMC8912962 DOI: 10.3389/fpls.2022.772685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/06/2022] [Indexed: 05/24/2023]
Abstract
Cucurbita pepo is one of the earliest cultivated crops. It is native to Central and South America and is now widely cultivated all over the world for its rich nutrition, short growth period, and high yield, which make it suitable for intercropping. Hull-less C. pepo L. (HLCP) is a rare variant in nature that is easier to consume. Its seed has a seed kernel but lacks a seed coat. The molecular mechanism underlying the lack of seed coat development in the HLCP variety is not clear yet. The BGISEQ-500 sequencing platform was used to sequence 18 cDNA libraries of seed coats from hulled C. pepo (CP) and HLCP at three developmental stages (8, 18, and 28 days) post-pollination. We found that lignin accumulation in the seed coat of the HLCP variety was much lower than that of the CP variety. A total of 2,099 DEGs were identified in the CP variety, which were enriched mainly in the phenylpropanoid biosynthesis pathway, amino sugar, and nucleotide sugar metabolism pathways. A total of 1,831 DEGs were identified in the HLCP variety and found to be enriched mainly in the phenylpropanoid biosynthesis and metabolism pathways of starch and sucrose. Among the DEGs, hub proteins (FusA), protein kinases (IRAK4), and several transcription factors related to seed coat development (MYB, bHLH, NAC, AP2/EREBP, WRKY) were upregulated in the CP variety. The relative expression levels of 12 randomly selected DEGs were determined using quantitative real-time PCR analysis and found to be consistent with those obtained using RNA-Seq, with a correlation coefficient of 0.9474. We found that IRAK4 protein kinases, AP2/EREBP, MYB, bHLH, and NAC transcription factors may play important roles in seed coat development, leading to the formation of HLCP.
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Affiliation(s)
- Yingyu Xue
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Zhiyan Shen
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Fei Tao
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Jingjiang Zhou
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Bingliang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, China
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Rifna E, Dwivedi M. Effect of pulsed ultrasound assisted extraction and aqueous acetone mixture on total hydrolysable tannins from pomegranate peel. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2021.101496] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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9
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Xiong X, Liu X, Zhu X, Tan Y, Wang Z, Xu J, Tu X, Rao Y, Duan J, Zhao W, Zhou M. A mutation in PHKG1 causes high drip loss and low meat quality in Chinese Ningdu yellow chickens. Poult Sci 2021; 101:101556. [PMID: 34852315 PMCID: PMC8639467 DOI: 10.1016/j.psj.2021.101556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/29/2021] [Accepted: 10/14/2021] [Indexed: 12/18/2022] Open
Abstract
With increasing societal development and the concurrent improvement in people's quality of life, meat consumption has gradually changed from a focus on “quantity” to “quality”. Broiler production is increasingly used as a means to improve meat quality by altering various characteristics, especially its genetic factors. However, until now, little has been known about the genetic variants related to meat quality traits in Chinese purebred chicken populations. To better understand these genetic underpinnings, a total of 17 traits related to meat quality and carcass were measured in 325 Chinese Ningdu yellow chickens. We performed DNA sequencing to detect nucleotide mutations, after which we conducted association studies between PHKG1 gene polymorphisms and traits related to meat quality and carcass. Results indicated a large phenotypic variation in meat quality traits. More specifically, the single nucleotide polymorphism (SNP) rs15845448 was significantly associated with drip loss at 24 h (P = 8.04 × 10−6) and 48 h (P = 5.47 × 10−6), pH (P = 2.39 × 10−3), and meat color L* (P = 9.88 × 10−3). Moreover, the SNP rs15845448 reduced 24 h and 48 h drip loss by 3.62 and 5.97%, respectively. However, no significant associations were found between rs15845448 and carcass traits (P > 0.05). Furthermore, a haplotype block containing 2 adjacent SNPs (rs15845448 and rs15845450) was identified. This block displayed 4 distinct haplotypes that had significant association with drip loss at 24 h and 48 h, pH, and meat color L*. Collectively, these results provide new insights into the genetic basis of meat quality in Chinese Ningdu yellow chickens. Moreover, the significance of SNP rs15845448 could be incorporated into the selection programs involving this breed.
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Affiliation(s)
- Xinwei Xiong
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Xianxian Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, China
| | - Xuenong Zhu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Yuwen Tan
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Zhangfeng Wang
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Jiguo Xu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Xutang Tu
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Yousheng Rao
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Jinhong Duan
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Wenliang Zhao
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China
| | - Min Zhou
- Institute of Biological Technology, Nanchang Normal University, Nanchang, 330032, China; Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang, 330032, China.
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10
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Poudel K, Luo X, Chen L, Jing D, Xia X, Tang L, Li H, Cao S. Identification of the SUT Gene Family in Pomegranate ( Punica granatum L.) and Functional Analysis of PgL0145810.1. Int J Mol Sci 2020; 21:ijms21186608. [PMID: 32927615 PMCID: PMC7554910 DOI: 10.3390/ijms21186608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 11/20/2022] Open
Abstract
Sucrose, an important sugar, is transported from source to sink tissues through the phloem, and plays important role in the development of important traits in plants. However, the SUT gene family is still not well characterized in pomegranate. In this study, we first identified the pomegranate sucrose transporter (SUT) gene family from the whole genome. Then, the phylogenetic relationship of SUT genes, gene structure and their promoters were analyzed. Additionally, their expression patterns were detected during the development of the seed. Lastly, genetic transformation and cytological observation were used to study the function of PgL0145810.1. A total of ten pomegranate SUT genes were identified from the whole genome of pomegranate ‘Tunisia’. The promoter region of all the pomegranate SUT genes contained myeloblastosis (MYB) elements. Four of the SUT genes, PgL0328370.1, PgL0099690.1, PgL0145810.1 and PgL0145770.1, were differentially expressed during seed development. We further noticed that PgL0145810.1 was expressed most prominently in the stem parts in transgenic plants compared to other tissue parts (leaves, flowers and silique). The cells in the xylem vessels were small and lignin content was lower in the transgenic plants as compared to wild Arabidopsis plants. In general, our result suggests that the MYB cis-elements in the promoter region might regulate PgL0145810.1 expression to control the structure of xylem, thereby affecting seed hardness in pomegranate.
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Belay ZA, Caleb OJ, Vorster A, van Heerden C, Opara UL. Transcriptomic changes associated with husk scald incidence on pomegranate fruit peel during cold storage. Food Res Int 2020; 135:109285. [PMID: 32527480 DOI: 10.1016/j.foodres.2020.109285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023]
Abstract
Pomegranate fruit is valued for its social, economic, aesthetic and health benefits. The fruit rapidly loses quality after harvest due to continued metabolic responses and physiological disorders under sub-optimal conditions. The incidence of physiological disorder such as husk scald manifests during storage and commercial shipping, which affects the appearance and limits marketability. Despite the importance of pomegranate husk scald, little information is available about the origin and molecular mechanisms. Therefore, the aim of this study was to investigate the scald incidence of pomegranate fruit at molecular level using RNA-Seq (Ion Proton™ Next Generation Sequencing) by analyzing peel transcriptomic changes. The RNA-seq analysis generated 98,441,278 raw reads. 652 Differentially Expressed Genes (DEGs) with a fold change of > |2|, a p value ≤ 0.05 and a false discovery rate (FDR) of <0.05 were identified between healthy and scald fruit peels. An analysis of the gene ontologies of these DEGs revealed the 432 genes were assigned with molecular functions, 272 as cellular components and 205 as part of biological processes. In this analysis, genes (Pgr023188 and Pgr025081) that encode uncharacterized protein and gene (Pgr007593) that encodes glycosyltransferase showed significantly highest fold changes. Genes (Pgr003448, Pgr006024 and Pgr023696) involved in various iron binding and oxidoreductase activities were significantly suppressed. This is the first transcriptome analysis of pomegranate fruit peel related to husk scald development. Results obtained from this study will add valuable information on husk scald related changes on pomegranate fruit at genomic level and provide insight on other related physiological disorders.
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Affiliation(s)
- Zinash A Belay
- Postharvest Technology Research Laboratory, South African Research Chair in Postharvest Technology, Department of Horticultural Science, Faculty of AgriSciences, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Oluwafemi J Caleb
- Agri-Food Systems and Omics Laboratory, Post-Harvest and Agro-Processing Technologies (PHATs), Agricultural Research Council (ARC) Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
| | - Alvera Vorster
- The Central Analytical Facilities (CAF), The DNA-sequencing Unit, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Carel van Heerden
- The Central Analytical Facilities (CAF), The DNA-sequencing Unit, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Umezuruike Linus Opara
- Postharvest Technology Research Laboratory, South African Research Chair in Postharvest Technology, Department of Horticultural Science, Faculty of AgriSciences, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa.
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12
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Luo X, Li H, Wu Z, Yao W, Zhao P, Cao D, Yu H, Li K, Poudel K, Zhao D, Zhang F, Xia X, Chen L, Wang Q, Jing D, Cao S. The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft- and hard-seeded cultivars. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:955-968. [PMID: 31549477 PMCID: PMC7061868 DOI: 10.1111/pbi.13260] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 09/03/2019] [Accepted: 09/09/2019] [Indexed: 05/18/2023]
Abstract
Complete and highly accurate reference genomes and gene annotations are indispensable for basic biological research and trait improvement of woody tree species. In this study, we integrated single-molecule sequencing and high-throughput chromosome conformation capture techniques to produce a high-quality and long-range contiguity chromosome-scale genome assembly of the soft-seeded pomegranate cultivar 'Tunisia'. The genome covers 320.31 Mb (scaffold N50 = 39.96 Mb; contig N50 = 4.49 Mb) and includes 33 594 protein-coding genes. We also resequenced 26 pomegranate varieties that varied regarding seed hardness. Comparative genomic analyses revealed many genetic differences between soft- and hard-seeded pomegranate varieties. A set of selective loci containing SUC8-like, SUC6, FoxO and MAPK were identified by the selective sweep analysis between hard- and soft-seeded populations. An exceptionally large selective region (26.2 Mb) was identified on chromosome 1. Our assembled pomegranate genome is more complete than other currently available genome assemblies. Our results indicate that genomic variations and selective genes may have contributed to the genetic divergence between soft- and hard-seeded pomegranate varieties.
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Affiliation(s)
- Xiang Luo
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Haoxian Li
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Zhikun Wu
- State Key Laboratory of OphthalmologyZhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouChina
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Da Cao
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Haiyan Yu
- Biomarker Technologies CorporationBeijingChina
| | - Kaidi Li
- Biomarker Technologies CorporationBeijingChina
| | - Krishna Poudel
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Diguang Zhao
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Fuhong Zhang
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Xiaocong Xia
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Lina Chen
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Qi Wang
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Dan Jing
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
| | - Shangyin Cao
- Chinese Academy of Agricultural SciencesZhengzhou Fruit Tree Research InstituteZhengzhouChina
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13
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Qin G, Liu C, Li J, Qi Y, Gao Z, Zhang X, Yi X, Pan H, Ming R, Xu Y. Diversity of metabolite accumulation patterns in inner and outer seed coats of pomegranate: exploring their relationship with genetic mechanisms of seed coat development. HORTICULTURE RESEARCH 2020; 7:10. [PMID: 31934341 PMCID: PMC6946660 DOI: 10.1038/s41438-019-0233-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/30/2019] [Accepted: 12/04/2019] [Indexed: 05/14/2023]
Abstract
The expanded outer seed coat and the rigid inner seed coat of pomegranate seeds, both affect the sensory qualities of the fruit and its acceptability to consumers. Pomegranate seeds are also an appealing model for the study of seed coat differentiation and development. We conducted nontarget metabolic profiling to detect metabolites that contribute to the morphological differentiation of the seed coats along with transcriptomic profiling to unravel the genetic mechanisms underlying this process. Comparisons of metabolites in the lignin biosynthetic pathway accumulating in seed coat layers at different developmental stages revealed that monolignols, including coniferyl alcohol and sinapyl alcohol, greatly accumulated in inner seed coats and monolignol glucosides greatly accumulated in outer seed coats. Strong expression of genes involved in monolignol biosynthesis and transport might explain the spatial patterns of biosynthesis and accumulation of these metabolites. Hemicellulose constituents and flavonoids in particular accumulated in the inner seed coat, and candidate genes that might be involved in their accumulation were also identified. Genes encoding transcription factors regulating monolignol, cellulose, and hemicellulose metabolism were chosen by coexpression analysis. These results provide insights into metabolic factors influencing seed coat differentiation and a reference for studying seed coat developmental biology and pomegranate genetic improvement.
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Affiliation(s)
- Gaihua Qin
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Anhui Province, Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
- Key Laboratory of Fruit Quality and Development Biology, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
| | - Chunyan Liu
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Anhui Province, Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
- Key Laboratory of Fruit Quality and Development Biology, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
| | - Jiyu Li
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Anhui Province, Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
- Key Laboratory of Fruit Quality and Development Biology, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
| | - Yongjie Qi
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Anhui Province, Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
- Key Laboratory of Fruit Quality and Development Biology, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
| | - Zhenghui Gao
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Anhui Province, Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
- Key Laboratory of Fruit Quality and Development Biology, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
| | - Xiaoling Zhang
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Anhui Province, Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
| | - Xingkai Yi
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Anhui Province, Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
| | - Haifa Pan
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Anhui Province, Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61822 USA
| | - Yiliu Xu
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crops, Anhui Province, Horticultural Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
- Key Laboratory of Fruit Quality and Development Biology, Anhui Academy of Agricultural Sciences, Hefei, 230001 China
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14
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Zhao XY, Qi CH, Jiang H, Zhong MS, You CX, Li YY, Hao YJ. MdHIR4 transcription and translation levels associated with disease in apple are regulated by MdWRKY31. PLANT MOLECULAR BIOLOGY 2019; 101:149-162. [PMID: 31267255 DOI: 10.1007/s11103-019-00898-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/26/2019] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE Here we describe that the regulation of MdWRKY31 on MdHIR4 in transcription and translation levels associated with disease in apple. The phytohormone salicylic acid (SA) is a main factor in apple (Malus domestica) production due to its function in disease resistance. WRKY transcription factors play a vital role in response to stress. An RNA-seq analysis was conducted with 'Royal Gala' seedlings treated with SA to identify the WRKY regulatory mechanism of disease resistance in apple. The analysis indicated that MdWRKY31 was induced. A quantitative real-time polymerase chain reaction (qPCR) analysis demonstrated that the expression of MdWRKY31 was induced by SA and flg22. Ectopic expression of MdWRKY31 in Arabidopsis and Nicotiana benthamiana increased the resistance to flg22 and Pseudomonas syringae tomato (Pst DC3000). A yeast two-hybrid screen was conducted to further analyze the function of MdWRKY31. As a result, hypersensitive-induced reaction (HIR) protein MdHIR4 interacted with MdWRKY31. Biomolecular fluorescence complementation, yeast two-hybrid, and pull-down assays demonstrated the interaction. In our previous study, MdHIR4 conferred decreased resistance to Botryosphaeria dothidea (B. dothidea). A viral vector-based transformation assay indicated that MdWRKY31 evaluated the transcription of SA-related genes, including MdPR1, MdPR5, and MdNPR1 in an MdHIR4-dependent way. A GUS analysis demonstrated that the w-box, particularly w-box2, of the MdHIR4 promoter played a major role in the responses to SA and B. dothidea. Electrophoretic mobility shift assays, yeast one-hybrid assay, and chromatin immunoprecipitation-qPCR demonstrated that MdWRKY31 directly bound to the w-box2 motif in the MdHIR4 promoter. GUS staining activity and a protein intensity analysis further showed that MdWRKY31 repressed MdHIR4 expression. Taken together, our findings reveal that MdWRKY31 regulated plant resistance to B. dothidea through the SA signaling pathway by interacting with MdHIR4.
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Affiliation(s)
- Xian-Yan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chen-Hui Qi
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Han Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ming-Shuang Zhong
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yuan-Yuan Li
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Yu-Jin Hao
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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15
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Fang X, Zhang Y, Zhang Y, Huang K, Yang W, Li X, Zhang Z, Wu K, Xu X, Ruan R, Yuan X, Zhang Z, Yi Z. De novo transcriptome assembly and identification of genes related to seed size in common buckwheat ( Fagopyrum esculentum M.). BREEDING SCIENCE 2019; 69:487-497. [PMID: 31598082 PMCID: PMC6776140 DOI: 10.1270/jsbbs.18194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/15/2019] [Indexed: 05/23/2023]
Abstract
Common buckwheat (Fagopyrum esculentum M.) belongs to the eudicot family Polygonaceae, Fagopyrum Mill, and its seeds have high nutritional value. The mechanism of seed development of common buckwheat remains unclear at the molecular level and no genes related to seed size have been identified. In this study, we performed genome-wide transcriptome sequencing and analysis using common buckwheat seeds at 5 days post anthesis (DPA) and 10 DPA from two cultivars (large-seeded and small-seeded). A total of 259,895 transcripts were assembled, resulting in 187,034 unigenes with average length of 1097 bp and N50 of 1538 bp. Based on gene expression profiles, 9127 differentially expressed genes (DEGs) were identified and analyzed in GO enrichment and KEGG analysis. In addition, genes related to seed size in the IKU pathway, ubiquitin-proteasome pathway, MAPK signaling pathway, TFs and phytohormones were identified and analyzed. AP2 and bZIP transcription factors, BR-signal and ABA were considered to be important regulators of seed size. This study provides a valuable genetic resource for future identification and functional analysis of candidate genes regulating seed size in common buckwheat and will be useful for improving seed yield in common buckwheat through molecular breeding in the future.
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Affiliation(s)
| | | | | | - Kehui Huang
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Wenjuan Yang
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Xiaoyu Li
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Zhiyong Zhang
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Kanghong Wu
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Xin Xu
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Renwu Ruan
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Xiaohui Yuan
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University,
Chongqing, 400716,
People’s Republic of China
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16
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Xia X, Li H, Cao D, Luo X, Yang X, Chen L, Liu B, Wang Q, Jing D, Cao S. Characterization of a NAC transcription factor involved in the regulation of pomegranate seed hardness (Punica granatum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:379-388. [PMID: 30954020 DOI: 10.1016/j.plaphy.2019.01.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
The pomegranate, Punica granatum L., which has been cultivated since antiquity, is known to be a superfruit, possessing an array of functional anti-oxidants and various other health benefits. The hardness of pomegranate seeds is an important indicator of fruit quality, which in turn affects economic value and market demand. However, the molecular mechanism underlying pomegranate seed hardness remains to be fully understood. In this study, we found a positive correlation between seed hardness and lignin content in two pomegranate varieties: "Tunisia" and "Sanbai". Specifically, genes associated with lignin biosynthesis were differentially expressed in soft-seed and hard-seed pomegranate varieties. Among these differential genes, we cloned and characterized the NAC transcription factor PgSND1-like. Sequence alignment found a single base replacement at the 166-bp position of CDS in the PgSND1-like gene from "Tunisia" and "Sanbai". Both PgSND1-like (Sanbai) and PgSND1-like (Tunisia) proteins are localized in the cell nucleus and have a transcription activation domain in the C-terminus. Yeast two-hybrid analysis indicated that PgSND1-like protein interacts with itself to form a homodimer. Overexpression of PgSND1-like (Sanbai) in Arabidopsis showed a higher lignin content in inflorescence stem and mature seed compared with wild-type Arabidopsis. Accordingly, the expression levels of several lignin biosynthesis-associated genes were upregulated in stem cells and mature seeds of transgenic plants. However, PgSND1-like (Tunisia) transgenic Arabidopsis showed no phenotypic differences with wild-type Arabidopsis. Taken together, we suggest that PgSND1-like may regulate at least two different functions in two pomegranate varieties, promoting lignin biosynthesis and seed hardness of pomegranate.
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Affiliation(s)
- Xiaocong Xia
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Haoxian Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Da Cao
- The University of Queensland , St Lucia, QLD 4072, Australia
| | - Xiang Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Xuanwen Yang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Lina Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Beibei Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Qi Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Dan Jing
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Shangyin Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China.
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17
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Luo X, Cao D, Zhang J, Chen L, Xia X, Li H, Zhao D, Zhang F, Xue H, Chen L, Li Y, Cao S. Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness. Sci Rep 2018; 8:9292. [PMID: 29915181 PMCID: PMC6006261 DOI: 10.1038/s41598-018-27664-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022] Open
Abstract
The breeding of new soft-seeded pomegranate cultivars provides new products for the market and increases farmers' incomes, yet the genetic architecture mediating seed hardness is largely unknown. Here, the seed hardness and hundred-seed weights of 26 cultivars were determined in 2 successive years. We conducted miRNA and mRNA sequencing to analyse the seeds of two varieties of Punica granatum: soft-seeded Tunisia and hard-seeded Sanbai, at 60 and 120 d after flowering. Seed hardness was strongly positively correlated with hundred-seed weight. We detected 25 and 12 differentially expressed miRNA-mRNA pairs with negative regulatory relationships between the two genotypes at 60 and 120 d after flowering, respectively. These miRNA-mRNA pairs mainly regulated seed hardness by altering cell wall structure. Transcription factors including NAC1, WRKY and MYC, which are involved in seed hardness, were targeted by differentially expressed mdm-miR164e and mdm-miR172b. Thus, seed hardness is the result of a complex biological process regulated by a miRNA-mRNA network in pomegranate. These results will help us understand the complexity of seed hardness and help to elucidate the miRNA-mediated molecular mechanisms that contribute to seed hardness in pomegranate.
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Affiliation(s)
- Xiang Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Da Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Jianfeng Zhang
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, P.R. China
| | - Li Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xiaocong Xia
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Haoxian Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Diguang Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Fuhong Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Hui Xue
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Lina Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China
| | - Yongzhou Li
- College of Horticultural Science, Henan Agricultural University, Zhengzhou, 450002, P.R. China
| | - Shangyin Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, P.R. China.
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18
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Wang H, Zhang Y, Tian Z, Ma J, Kang M, Ding C, Ming D. Preparation of β-CD-Ellagic Acid Microspheres and Their Effects on HepG2 Cell Proliferation. Molecules 2017; 22:molecules22122175. [PMID: 29292740 PMCID: PMC6149914 DOI: 10.3390/molecules22122175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/29/2017] [Accepted: 12/06/2017] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE In this study, β-cyclodextrin (β-CD) was chosen as the coating for ellagic acid to prepare ellagic acid microspheres, and the effect of microspheres on the growth of HepG2 cells was observed. METHODS Scanning electron microscopy, infrared spectroscopy, and release rate analysis were used to identify the formation of ellagic acid microspheres. Methyl thiazolyl tetrazolium (MTT) assay was used to detect the effect of different concentrations of ellagic acid microspheres on tumor cell proliferation at 6, 12, 24 and 36 h, and cell morphology and quantity were observed using hematoxylin-eosin (HE) staining. Single-cell gel electrophoresis was used to observe the effect of ellagic acid microspheres on the DNA damage of HepG2 cells, and the Olive tail moment and the mRNA expression of tumor suppressor protein gene p53 was measured. RESULTS β-CD could be used as wrapping material of ellagic acid to prepare ellagic acid microspheres. HepG2 cell proliferation could be inhibited by 0.1, 0.3 and 0.5 g/L of ellagic acid microspheres in a dose- and time-dependent manner, and the mechanism of proliferation inhibition was related to DNA damage and cell apoptosis. CONCLUSION Preparing ellagic acid microspheres with β-CD is feasible, and ellagic acid microspheres have potential therapeutic value (anticancer).
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Affiliation(s)
- Hongkai Wang
- College of Life Science, Zaozhuang University, Zaozhuang 277160, China.
| | - Yingxia Zhang
- College of Life Science, Zaozhuang University, Zaozhuang 277160, China.
| | - Zhongjing Tian
- College of Life Science, Zaozhuang University, Zaozhuang 277160, China.
| | - Jing Ma
- College of Medical Science, Zaozhuang Vocational College, Zaozhuang 277800, China.
| | - Meiling Kang
- College of Life Science, Zaozhuang University, Zaozhuang 277160, China.
| | - Chengshi Ding
- College of Life Science, Zaozhuang University, Zaozhuang 277160, China.
| | - Dongfeng Ming
- College of Life Science, Zaozhuang University, Zaozhuang 277160, China.
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