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Rajpal VR, Sehgal D, Valluru R, Singh S. Editorial: Current advances in genomics and gene editing tools for crop improvement in a changing climate scenario. Front Genet 2023; 14:1214679. [PMID: 37377598 PMCID: PMC10291607 DOI: 10.3389/fgene.2023.1214679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Affiliation(s)
- Vijay Rani Rajpal
- Depatment of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Deepmala Sehgal
- Syngenta, Jeolett’s Hill International Research Center, Bracknell, United Kingdom
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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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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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Li J, Liu C, Yu Q, Cao Z, Yang Y, Jia B, Su Y, Li G, Qin G. Identification of sugar transporter (SWEET) genes involved in pomegranate seed coat sugar accumulation. 3 Biotech 2022; 12:181. [PMID: 35875178 PMCID: PMC9296756 DOI: 10.1007/s13205-022-03248-6] [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: 12/28/2021] [Accepted: 07/02/2022] [Indexed: 11/30/2022] Open
Abstract
Sugar content of the outer seed coat and hardness of the inner seed coat are important traits of the pomegranate fruit. The translocation of sugars across biological membranes, mediated by SWEET transporters, is critical to seed development. In this study, we identified 16 PgrSWEET genes distributed on six chromosomes in the pomegranate genome. According to the phylogenetic analysis, PgrSWEET proteins were divided into four groups. Tandem and segmental duplications contributed to the expansion of the PgrSWEET family, while functional redundancy and diversification may have occurred among SWEET members according to analyses of evolution and gene expression. RNA-seq and qRT-PCR analyses revealed that PgrSWEET1a and PgrSWEET9 were highly expressed in the inner seed coat, and the expression levels gradually increased during seed development. Moreover, the relative expression levels of PgrSWEET1a and PgrSWEET9 in a hard-seeded cultivar were higher than those in a soft-seeded cultivar, indicating that PgrSWEET1a and PgrSWEET9 might function in the inner seed coat development by accumulating sugar metabolites. We also found that PgrSWEET2 was highly expressed in the outer seed coat during seed development, and the protein was localized to the tonoplast, indicating that PgrSWEET2 is likely a candidate regulating sugar accumulation or reutilization in the vacuoles of the outer seed coat. Genes encoding transcription factors probably regulating the candidate PgrSWEET genes were chosen by co-expression analysis. These results not only helped to characterize PgrSWEET genes but also provided an insight into their functions in relation to seed coat development. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03248-6.
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Affiliation(s)
- Jiyu Li
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
- Key Laboratory of Fruit Quality and Developmental Biology, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Chunyan Liu
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
- Key Laboratory of Fruit Quality and Developmental Biology, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Qing Yu
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
- Key Laboratory of Fruit Quality and Developmental Biology, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Zhen Cao
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
- Key Laboratory of Fruit Quality and Developmental Biology, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Yuan Yang
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
- Key Laboratory of Fruit Quality and Developmental Biology, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Botao Jia
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
- Key Laboratory of Fruit Quality and Developmental Biology, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Ying Su
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
- Key Laboratory of Fruit Quality and Developmental Biology, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Guixiang Li
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
- Key Laboratory of Fruit Quality and Developmental Biology, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Gaihua Qin
- Key Laboratory of Horticultural Crop Genetic Improvement and Eco-Physiology of Anhui Province, Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
- Key Laboratory of Fruit Quality and Developmental Biology, Anhui Academy of Agricultural Sciences, Hefei, 230031 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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Dhaka N, Sharma R. MicroRNA-mediated regulation of agronomically important seed traits: a treasure trove with shades of grey! Crit Rev Biotechnol 2021; 41:594-608. [PMID: 33682533 DOI: 10.1080/07388551.2021.1873238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Seed development is an intricate process with multiple levels of regulation. MicroRNAs (miRNAs) have emerged as one of the crucial components of molecular networks underlying agronomically important seed traits in diverse plant species. In fact, loss of function of the genes regulating miRNA biogenesis also exhibits defects in seed development. A total of 21 different miRNAs have experimentally been shown to regulate seed size, nutritional content, vigor, and shattering, and have been reviewed here. The mechanism details of the associated regulatory cascades mediated through transcriptional regulators, phytohormones, basic metabolic machinery, and secondary siRNAs are elaborated. Co-localization of miRNAs and their target regions with seed-related QTLs provides new avenues for engineering these traits using conventional breeding programs or biotechnological interventions. While global analysis of miRNAs using small RNA sequencing studies are expanding the repertoire of candidate miRNAs, recent revelations on their inheritance, transport, and mechanism of action would be instrumental in designing better strategies for optimizing agronomically relevant seed traits.
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Affiliation(s)
- Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Haryana, India.,Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rita Sharma
- Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Kaseke T, Fawole OA, Mokwena L, Opara UL. Effect of cultivar and blanching of pomegranate seeds on physicochemical properties, nutritional qualities and antioxidant capacity of extracted oil. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2021. [DOI: 10.1007/s11694-020-00615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kaseke T, Opara UL, Fawole OA. Effect of Microwave Pretreatment of Seeds on the Quality and Antioxidant Capacity of Pomegranate Seed Oil. Foods 2020; 9:E1287. [PMID: 32937735 PMCID: PMC7555658 DOI: 10.3390/foods9091287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 08/29/2020] [Accepted: 09/06/2020] [Indexed: 11/21/2022] Open
Abstract
Microwave pretreatment of oilseeds is a novel technique used to enhance oil nutraceutical properties. In this study, the effect of microwave pretreatment of seeds was investigated on pomegranate seed oil quality attributes including oil yield, yellowness index, refractive index, peroxide value, ρ-anisidine value, total oxidation value, conjugated dienes, total phenolic content, total carotenoids content, phytosterol composition, fatty acid composition, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity, and ferric reducing antioxidant power (FRAP). The seeds of three different pomegranate cultivars ('Acco', 'Herskawitz', and 'Wonderful') were microwave heated at 261 W for 102 s. Pomegranate seeds microwave pretreatment enhanced oil yield, yellowness index, total carotenoids content, total phenolic content, FRAP and DPPH radical scavenging capacity, despite an increase in conjugated dienes, and peroxide value. Palmitic acid, oleic acid, linoleic acid, saturated, and monosaturated fatty acids were increased after pomegranate seeds microwave pretreatment, whilst the levels of punicic acid and β-sitosterol were reduced. Nevertheless, the refractive index, the ratio of unsaturated to saturated fatty acid of the extracted oil were not significantly (p > 0.05) affected by pomegranate seeds microwave pretreatment. Principal component analysis and agglomerative hierarchical clustering established that 'Acco' and 'Wonderful' oil extracts from microwave pretreated PS exhibited better oil yield, whilst 'Herskawitz' oil extracts showed higher total carotenoids content, total phenolic content, and antioxidant capacity.
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Affiliation(s)
- Tafadzwa Kaseke
- Postharvest Technology Research Laboratory, Department of Food Science, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7602, South Africa;
| | - Umezuruike Linus Opara
- Postharvest Technology Research Laboratory, Department of Food Science, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7602, South Africa;
- Postharvest Technology Research Laboratory, Department of Horticultural Sciences, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Olaniyi Amos Fawole
- Postharvest Research Laboratory, Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg 2006, South Africa
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9
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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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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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Chen L, Luo X, Yang X, Jing D, Xia X, Li H, Poudel K, Cao S. Small RNA and mRNA Sequencing Reveal the Roles of microRNAs Involved in Pomegranate Female Sterility. Int J Mol Sci 2020; 21:ijms21020558. [PMID: 31952315 PMCID: PMC7013964 DOI: 10.3390/ijms21020558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 11/18/2022] Open
Abstract
Female sterility is a key factor restricting plant reproduction. Our previous studies have revealed that pomegranate female sterility mainly arose from the abnormality of ovule development. MicroRNAs (miRNAs) play important roles in ovule development. However, little is known about the roles of miRNAs in female sterility. In this study, a combined high-throughput sequencing approach was used to investigate the miRNAs and their targeted transcripts involved in female development. A total of 103 conserved and 58 novel miRNAs were identified. Comparative profiling indicated that the expression of 43 known miRNAs and 14 novel miRNAs were differentially expressed between functional male flowers (FMFs) and bisexual flowers (BFs), 30 known miRNAs and nine novel miRNAs showed significant differences among different stages of BFs, and 20 known miRNAs and 18 novel miRNAs exhibited remarkable expression differences among different stages of FMFs. Gene ontology (GO) analyses of 144 predicted targets of differentially expressed miRNAs indicated that the “reproduction process” and “floral whorl development” processes were significantly enriched. The miRNA–mRNA interaction analyses revealed six pairs of candidate miRNAs and their targets associated with female sterility. Interestingly, pg-miR166a-3p was accumulated, whereas its predicted targets (Gglean012177.1 and Gglean013966.1) were repressed in functional male flowers (FMFs), and the interaction between pg-miR166a-3p and its targets (Gglean012177.1 and Gglean013966.1) were confirmed by transient assay. A. thaliana transformed with 35S-pre-pg-miR166a-3p verified the role of pg-miR166a-3p in ovule development, which indicated pg-miR166a-3p’s potential role in pomegranate female sterility. The results provide new insights into molecular mechanisms underlying the female sterility at the miRNA level.
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12
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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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