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Liu H, Zhang X, Li J, Zhang G, Fang H, Li Y. Transcriptome analysis reveals the mechanism of different fruit appearance between apricot (Armeniaca vulgaris Lam.) and its seedling. Mol Biol Rep 2023; 50:7995-8003. [PMID: 37540452 DOI: 10.1007/s11033-023-08631-x] [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: 04/22/2023] [Accepted: 06/26/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Apricot fruit has great economic value. In the process of apricot breeding using traditional breeding methods, we obtained a larger seedling (named Us) from the original variety (named U). And Us fruit is larger than U, taste better. Therefore, revealing its mechanism is very important for Apricot breeding. METHODS In this study, de novo assembly and transcriptome sequencing (RNA-Seq) was used to screen the differently expressed genes (DEGs) between U and Us at three development stages, including young fruits stage, mid-ripening stage and mature fruit stage. RESULTS The results showed that there were 6,753 DEGs at different sampling time. "Cellulose synthase (UDP-forming) activity" and "cellulose synthase activity" were the key GO terms enriched in GO, of which CESA and CSL family played a key role. "Photosynthesis-antenna proteins" and "Plant hormone signal transduction" were the candidate pathways and lhca, lhcb, Aux/IAA and SAUR were the main regulators. CONCLUSION The auxin signaling pathway was active in Us, of which Aux/IAAs and SAUR were the key fruit size regulators. The low level of lhca and lhcb in Us could reveal the low demand for exogenous carbon, but they increased at mature stage, which might be due to the role of aux, who was keeping the fruit growing. Aux and photosynthesis maight be the main causes of appearance formation of Us fruits. Interestingly, the higher expression of CESA and CSL proved that Us entered the hardening process earlier than U. The advanced developmental progress might also be due to the role of Aux.
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Affiliation(s)
- Huiyan Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, China
| | - Xiangjun Zhang
- School of Life Science, Ningxia University, Yinchuan, 750021, China
| | - Jianshe Li
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, China
- Ningxia Facility Horticulture Engineering Technology Center, Yinchuan, 750021, China
- Technological Innovation Center of Horticulture (Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, 750021, China
| | - Guangdi Zhang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, China.
- Ningxia Facility Horticulture Engineering Technology Center, Yinchuan, 750021, China.
- Technological Innovation Center of Horticulture (Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, 750021, China.
| | - Haitian Fang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, China.
| | - Yu Li
- Technological Innovation Center of Horticulture (Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, 750021, China
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Iqbal S, Bai Y, Hayat F, Coulibaly D, Khalil-Ur-Rehman M, Shi T, Gao Z. Comprehensive transcriptomic and metabolomic analysis revealed distinct flavonoid biosynthesis regulation during abnormal pistil development in Japanese apricot. Genomics 2022; 114:110451. [PMID: 35988654 DOI: 10.1016/j.ygeno.2022.110451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 08/06/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022]
Abstract
Japanese apricot is an imperative stone fruit plant with numerous processing importance. The failure of reproductive system is the most common cause of fruit loss, through which pistil abortion is the fundamental one. To understand this mechanism, we used a combination of transcriptomic and metabolomic approaches to investigate the biochemical and molecular basis of flavonoid biosynthesis. Due to the regulated expression of flavonoid pathway-related genes in plants, flavonoid biosynthesis is largely regulated at the transcriptional level. A total of 2272 differently expressed genes and 215 differential metabolites were found. The expression of the genes and metabolites encoding flavonoid biosynthesis was lower in abnormal pistils that are in line with the flavonoid quantification from abnormal pistils. Besides, a couple of genes were also detected related to MYB, MADS, NAC and bHLH transcription factors. Remarkably, we found 'hydroxycinnamoyl transferase (LOC103323133)' and flavonoid related metabolite '2-hydroxycinnamic acid' was lower expressed in abnormal pistil, proposing the cause of pistil abortion. Collectively, the present study delivers inclusive transcriptional and metabolic datasets that proposed valuable prospects to unravel the genetic mechanism underlying pistil abortion.
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Affiliation(s)
- Shahid Iqbal
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
| | - Yang Bai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Faisal Hayat
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Daouda Coulibaly
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | | | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Iqbal S, Hayat F, Mushtaq N, Khalil-ur-Rehman M, Khan U, Yasoob TB, Khan MN, Ni Z, Ting S, Gao Z. Bioinformatics Study of Aux/IAA Family Genes and Their Expression in Response to Different Hormones Treatments during Japanese Apricot Fruit Development and Ripening. PLANTS 2022; 11:plants11151898. [PMID: 35893602 PMCID: PMC9332017 DOI: 10.3390/plants11151898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022]
Abstract
Auxin/indole-3-acetic acid (Aux/IAA) is a transcriptional repressor in the auxin signaling pathway that plays a role in several plant growth and development as well as fruit and embryo development. However, it is unclear what role they play in Japanese apricot (Prunus mume) fruit development and maturity. To investigate the role of Aux/IAA genes in fruit texture, development, and maturity, we comprehensively identified and expressed 19 PmIAA genes, and demonstrated their conserved domains and homology across species. The majority of PmIAA genes are highly responsive and expressed in different hormone treatments. PmIAA2, PmIAA5, PmIAA7, PmIAA10, PmIAA13, PmIAA18, and PmIAA19 showed a substantial increase in expression, suggesting that these genes are involved in fruit growth and maturity. During fruit maturation, alteration in the expression of PmIAA genes in response to 1-Methylcyclopropene (1-MCP) treatment revealed an interaction between auxin and ethylene. The current study investigated the response of Aux/IAA development regulators to auxin during fruit ripening, with the goal of better understanding their potential application in functional genomics.
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Affiliation(s)
- Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
- Correspondence: (S.I.); (Z.G.); Tel./Fax: +86-025-8439-5724 (S.I. & Z.G.)
| | - Faisal Hayat
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China;
| | - Naveed Mushtaq
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
| | - Muhammad Khalil-ur-Rehman
- Department of Horticultural Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Ummara Khan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China;
| | - Talat Bilal Yasoob
- Department of Animal Sciences, Ghazi University, Dera Ghazi Khan 32200, Pakistan;
| | | | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
| | - Shi Ting
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (N.M.); (Z.N.); (S.T.)
- Correspondence: (S.I.); (Z.G.); Tel./Fax: +86-025-8439-5724 (S.I. & Z.G.)
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Shirasawa K, Esumi T, Itai A, Isobe S. Cherry Blossom Forecast Based on Transcriptome of Floral Organs Approaching Blooming in the Flowering Cherry ( Cerasus × yedoensis) Cultivar 'Somei-Yoshino'. FRONTIERS IN PLANT SCIENCE 2022; 13:802203. [PMID: 35154222 PMCID: PMC8825344 DOI: 10.3389/fpls.2022.802203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
To gain insights into the genetic mechanisms underlying blooming and petal movement in flowering cherry (Cerasus × yedoensis), we performed time-course RNA-seq analysis of the floral buds and open-flowers of the most popular flowering cherry cultivar, 'Somei-Yoshino.' Independent biological duplicate samples of floral buds and open-flowers were collected from 'Somei-Yoshino' trees grown at three different locations in Japan. RNA-seq reads obtained from floral bud and open-flower samples collected in the current study (in 2019) and in a previous study (in 2017) were aligned against the genome sequence of 'Somei-Yoshino' to quantify gene transcript levels. Clustering analysis of RNA-seq reads revealed dynamic changes in the transcriptome, with genes in seven modules predominantly expressed at specific time points, ranging from 5 weeks before flowering to 2 weeks after flowering. Based on the identified gene modules and Gene Ontology (GO) terms enriched at different floral stages, we speculate that the genetic mechanisms underlying petal movement and flower opening in cherry involve the processes of development, cell wall organization, reproduction, and metabolism, which are executed by genes encoding transcription factors, phytohormones, transporters, and polysaccharide metabolic enzymes. Furthermore, we established a statistical model for cherry bloom forecasting, based on gene expression levels as RNA markers at different time points before flowering.
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Affiliation(s)
- Kenta Shirasawa
- Laboratory of Plant Genetics and Genomics, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Tomoya Esumi
- Laboratory of Pomology and Viticulture, Academic Assembly Institute of Agricultural and Life Sciences, Shimane University, Matsue, Japan
| | - Akihiro Itai
- Laboratory of Plant Resource Science, Department of Agricultural and Life Science, Kyoto Prefectural University, Kyoto, Japan
| | - Sachiko Isobe
- Laboratory of Plant Genetics and Genomics, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
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