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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 18976

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Prof. Dr. Yonghua Qin

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College of Horticulture, South China Agricultural University, Guangzhou 510642, China
Interests: tropical fruit; cultivar breeding; cultivation; physiology and biotechnology; microRNAs; transcriptomics; genomics; proteomics; metabolomics; genetics; fruit cultivar selection; fruit molecular biology
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Guibing Hu

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Guest Editor

College of Horticulture, South China Agricultural University, Guangzhou 510642, China
Interests: tropical fruit; cultivar breeding; cultivation; physiology and biotechnology; microRNAs; transcriptomics; genomics; proteomics; metabolomics; genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Tropical fruits are grown in hot and humid regions surrounding the Equator, as far north as the Tropic of Cancer and as far south as the Tropic of Capricorn. It is estimated that there are more than 300 tropical fruit crops that produce edible fruits, such as banana, pineapple, lychee, longan, mango, dragon fruit, passion fruit, papaya, rambutan, acai, jackfruit, mangosteen, avocado, guava, durian, cherimoya, cashew, macadamia nut, etc. Many developing countries are dependent on tropical fruits for their export and income, as well as their high nutritional value. Tropical fruit planting and production are growing globally. Tropical fruits are perishable crops and typically very sensitive to environmental, biotic, and abiotic stresses. Therefore, more pomologists are focusing on molecular research to learn how growth and development work and how to sustain the growth of tropical fruit crops in a sustainable way.

An upcoming Special Issue titled "Molecular Research of Tropical Fruit" will focus on the molecular mechanisms of tropical fruit production, growth and development, postharvest, genetics, and breeding, in an effort to address the primary issues faced by tropical fruit-producing countries. The main themes focus on the molecular research of tropical fruit crops on alternate bearing, flowering, fruit set, pruning, thinning, fertilization/irrigation/water relations, biostimulants and plant growth regulators, environment, postharvest, biotechnology and physiology, genetic resources, and breeding, etc. Topics include, but are not limited to, gene discovery and function, population genetics, genome projects, comparative and functional genomics, the molecular analysis of simple and complex genetic traits, developmental genetics, regulatory variation in gene expression, evolution, gene expression, and chromosome biology.

We invite agriculturists to contribute both reviews and original research articles to this Special Issue and to share your achievements in the field of the molecular research of tropical fruits.

Prof. Dr. Yonghua Qin
Prof. Dr. Guibing Hu
Guest Editors

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Keywords

tropical fruits
molecular research (microRNAs, genomics, transcriptomics, and proteomics)
cultivation
flowering
growth and development
fruit set and development
postharvest
biotechnology and physiology
genetics

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Published Papers (10 papers)

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16 pages, 6166 KiB

Open AccessArticle

EjFAD8 Enhances the Low-Temperature Tolerance of Loquat by Desaturation of Sulfoquinovosyl Diacylglycerol (SQDG)

by Xun Xu, Hao Yang, Xiaodong Suo, Mingxiu Liu, Danlong Jing, Yin Zhang, Jiangbo Dang, Di Wu, Qiao He, Yan Xia, Shuming Wang, Guolu Liang and Qigao Guo

Int. J. Mol. Sci. 2023, 24(8), 6946; https://doi.org/10.3390/ijms24086946 - 8 Apr 2023

Cited by 3 | Viewed by 1979

Abstract

Loquat (Eriobotrya japonica Lindl.) is an evergreen fruit tree of Chinese origin, and its autumn–winter flowering and fruiting growth habit means that its fruit development is susceptible to low-temperature stress. In a previous study, the triploid loquat (B431 × GZ23) has been identified with high photosynthetic efficiency and strong resistance under low-temperature stress. Analysis of transcriptomic and lipidomic data revealed that the fatty acid desaturase gene EjFAD8 was closely associated with low temperatures. Phenotypic observations and measurements of physiological indicators in Arabidopsis showed that overexpressing-EjFAD8 transgenic plants were significantly more tolerant to low temperatures compared to the wild-type. Heterologous overexpression of EjFAD8 enhanced some lipid metabolism genes in Arabidopsis, and the unsaturation of lipids was increased, especially for SQDG (16:0/18:1; 16:0/18:3), thereby improving the cold tolerance of transgenic lines. The expression of ICE-CBF-COR genes were further analyzed so that the relationship between fatty acid desaturase and the ICE-CBF-COR pathway can be clarified. These results revealed the important role of EjFAD8 under low-temperature stress in triploid loquat, the increase expression of FAD8 in loquat under low temperatures lead to desaturation of fatty acids. On the one hand, overexpression of EjFAD8 in Arabidopsis increased the expression of ICE-CBF-COR genes in response to low temperatures. On the other hand, upregulation of EjFAD8 at low temperatures increased fatty acid desaturation of SQDG to maintain the stability of photosynthesis under low temperatures. This study not only indicates that the EjFAD8 gene plays an important role in loquat under low temperatures, but also provides a theoretical basis for future molecular breeding of loquat for cold resistance. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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28 pages, 13706 KiB

Open AccessArticle

The Pitaya Flower Tissue’s Gene Differential Expression Analysis between Self-Incompatible and Self-Compatible Varieties for the Identification of Genes Involved in Self-Incompatibility Regulation

by Zhouwen Wang, Meng Wang, Yi Ding, Tao Li, Senrong Jiang, Shaoling Kang, Shuangshuang Wei, Jun Xie, Jiaquan Huang, Wenbin Hu, Hongli Li and Hua Tang

Int. J. Mol. Sci. 2023, 24(14), 11406; https://doi.org/10.3390/ijms241411406 - 13 Jul 2023

Cited by 1 | Viewed by 1729

Abstract

Self-incompatible pitaya varieties have low fruit-setting rates under natural conditions, leading to higher production costs and hindering industrial prosperity. Through transcriptome sequencing, we obtained the 36,900 longest transcripts (including 9167 new transcripts) from 60 samples of flowers. Samples were collected pre- and post-pollination (at 0 h, 0.5 h, 2 h, 4 h, and 12 h) from two varieties of pitaya (self-compatible Jindu No. 1 and self-incompatible Cu Sha). Using the RNA-Seq data and comparison of reference genomes, we annotated 28,817 genes in various databases, and 1740 genes were optimized in their structure for annotation. There were significant differences in the expression of differentially expressed genes (DEGs) in the pitaya stigmas under different pollination types, especially at the late post-pollination stage, where the expression of protease genes increasedal significantly under cross-pollination. We identified DEGs involved in the ribosomal, ubiquitination-mediated, and phyto-signaling pathways that may be involved in pitaya SI regulation. Based on the available transcriptome data and bioinformatics analysis, we tentatively identified HuS-RNase2 as a candidate gynogenetic S gene in the pitaya GSI system. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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28 pages, 7698 KiB

Open AccessReview

Pitaya Nutrition, Biology, and Biotechnology: A Review

by Kamran Shah, Jiayi Chen, Jiaxuan Chen and Yonghua Qin

Int. J. Mol. Sci. 2023, 24(18), 13986; https://doi.org/10.3390/ijms241813986 - 12 Sep 2023

Cited by 18 | Viewed by 5747

Abstract

Pitaya (Hylocereus spp.) is a member of the cactus family that is native to Central and South America but is now cultivated throughout the sub-tropical and tropical regions of the world. It is of great importance due to its nutritional, ornamental, coloring, medicinal, industrial, and high consumption values. In order to effectively utilize and develop the available genetic resources, it is necessary to appreciate and understand studies pertaining to the usage, origin, nutrition, diversity, evaluation, characterization, conservation, taxonomy, and systematics of the genus Hylocereus. Additionally, to gain a basic understanding of the biology of the plant, this review has also discussed how biotechnological tools, such as cell and tissue culture, micropropagation (i.e., somatic embryogenesis, organogenesis, somaclonal variation, mutagenesis, androgenesis, gynogenesis, and altered ploidy), virus-induced gene silencing, and molecular marker technology, have been used to enhance pitaya germplasm. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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13 pages, 1980 KiB

Open AccessArticle

Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (Citrullus lanatus)

by Yongtao Yu, Yuxiang Liufu, Yi Ren, Jie Zhang, Maoying Li, Shouwei Tian, Jinfang Wang, Shengjin Liao, Guoyi Gong, Haiying Zhang and Shaogui Guo

Int. J. Mol. Sci. 2023, 24(20), 15333; https://doi.org/10.3390/ijms242015333 - 18 Oct 2023

Cited by 1 | Viewed by 1663

Abstract

Fruit ripening is a highly complicated process that is accompanied by the formation of fruit quality. In recent years, a series of studies have demonstrated post-transcriptional control play important roles in fruit ripening and fruit quality formation. Till now, the post-transcriptional mechanisms for watermelon fruit ripening have not been comprehensively studied. In this study, we conducted PacBio single-molecule long-read sequencing to identify genome-wide alternative splicing (AS), alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) in watermelon fruit. In total, 6,921,295 error-corrected and mapped full-length non-chimeric (FLNC) reads were obtained. Notably, more than 42,285 distinct splicing isoforms were derived from 5,891,183 intron-containing full-length FLNC reads, including a large number of AS events associated with fruit ripening. In addition, we characterized 21,506 polyadenylation sites from 11,611 genes, 8703 of which have APA sites. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that fructose and mannose metabolism, starch and sucrose metabolism and carotenoid biosynthesis were both enriched in genes undergoing AS and APA. These results suggest that post-transcriptional regulation might potentially have a key role in regulation of fruit ripening in watermelon. Taken together, our comprehensive PacBio long-read sequencing results offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of watermelon fruit ripening. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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23 pages, 5933 KiB

Open AccessArticle

Integration of Metabolomics and Transcriptomics to Explore Dynamic Alterations in Fruit Color and Quality in ‘Comte de Paris’ Pineapples during Ripening Processes

by Kanghua Song, Xiumei Zhang, Jiameng Liu, Quansheng Yao, Yixing Li, Xiaowan Hou, Shenghui Liu, Xunxia Qiu, Yue Yang, Li Chen, Keqian Hong and Lijing Lin

Int. J. Mol. Sci. 2023, 24(22), 16384; https://doi.org/10.3390/ijms242216384 - 16 Nov 2023

Viewed by 1386

Abstract

Pineapple color yellowing and quality promotion gradually manifest as pineapple fruit ripening progresses. To understand the molecular mechanism underlying yellowing in pineapples during ripening, coupled with alterations in fruit quality, comprehensive metabolome and transcriptome investigations were carried out. These investigations were conducted using pulp samples collected at three distinct stages of maturity: young fruit (YF), mature fruit (MF), and fully mature fruit (FMF). This study revealed a noteworthy increase in the levels of total phenols and flavones, coupled with a concurrent decline in lignin and total acid contents as the fruit transitioned from YF to FMF. Furthermore, the analysis yielded 167 differentially accumulated metabolites (DAMs) and 2194 differentially expressed genes (DEGs). Integration analysis based on DAMs and DEGs revealed that the biosynthesis of plant secondary metabolites, particularly the flavonol, flavonoid, and phenypropanoid pathways, plays a pivotal role in fruit yellowing. Additionally, RNA-seq analysis showed that structural genes, such as FLS, FNS, F3H, DFR, ANR, and GST, in the flavonoid biosynthetic pathway were upregulated, whereas the COMT, CCR, and CAD genes involved in lignin metabolism were downregulated as fruit ripening progressed. APX as well as PPO, and ACO genes related to the organic acid accumulations were upregulated and downregulated, respectively. Importantly, a comprehensive regulatory network encompassing genes that contribute to the metabolism of flavones, flavonols, lignin, and organic acids was proposed. This network sheds light on the intricate processes that underlie fruit yellowing and quality alterations. These findings enhance our understanding of the regulatory pathways governing pineapple ripening and offer valuable scientific insight into the molecular breeding of pineapples. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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15 pages, 6216 KiB

Open AccessArticle

Integrative Analysis of Metabolome and Transcriptome Provides Insights into the Mechanism of Flower Induction in Pineapple (Ananas comosus (L.) Merr.) by Ethephon

by Wenqiu Lin, Shenghui Liu, Xiou Xiao, Weisheng Sun, Xinhua Lu, Yuyao Gao, Junjun He, Zhuying Zhu, Qingsong Wu and Xiumei Zhang

Int. J. Mol. Sci. 2023, 24(24), 17133; https://doi.org/10.3390/ijms242417133 - 5 Dec 2023

Viewed by 1245

Abstract

Exogenous ethylene is commonly utilized to initiate flower induction in pineapple (Ananas comosus (L.) Merr.). However, the molecular mechanisms and metabolic changes involved are not well understood. In this study, we explored the genetic network and metabolic shifts in the ‘Comte de Paris’ pineapple variety during ethylene-induced flowering. This was achieved through an integrative analysis of metabolome and transcriptome profiles at vegetative shoot apexes (0 d after ethephon treatment named BL_0d), the stage of bract primordia (8 d after ethephon treatment named BL_8d), stage of flower primordia (18 d after ethephon treatment named BL_18d), and the stage of stopped floret differentiation (34 d after ethephon treatment named BL_34d). We isolated and identified 804 metabolites in the pineapple shoot apex and inflorescence, categorized into 24 classes. Notably, 29, 31, and 46 metabolites showed significant changes from BL_0d to BL_8d, BL_8d to BL_18d, and BL_18d to BL_34d, respectively. A marked decrease in indole was observed, suggesting its role as a characteristic metabolite during flower induction. Transcriptomic analysis revealed 956, 1768, and 4483 differentially expressed genes (DEGs) for BL_0d vs. BL_8d, BL_8d vs. BL_18d, and BL_18d vs. BL_34d, respectively. These DEGs were significantly enriched in carbohydrate metabolism and hormone signaling pathways, indicating their potential involvement in flower induction. Integrating metabolomic and transcriptomic data, we identified several candidate genes, such as Agamous-Like9 (AGL9), Ethylene Insensitive 3-like (ETIL3), Apetala2 (AP2), AP2-like ethylene-responsive transcription factor ANT (ANT), and Sucrose synthase 2 (SS2), that play potentially crucial roles in ethylene-induced flower induction in pineapple. We also established a regulatory network for pineapple flower induction, correlating metabolites and DEGs, based on the Arabidopsis thaliana pathway as a reference. Overall, our findings offer a deeper understanding of the metabolomic and molecular mechanisms driving pineapple flowering. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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22 pages, 10531 KiB

Open AccessArticle

Kiwifruit Monodehydroascorbate Reductase 3 Gene Negatively Regulates the Accumulation of Ascorbic Acid in Fruit of Transgenic Tomato Plants

by Dongfeng Jia, Huan Gao, Yanqun He, Guanglian Liao, Liting Lin, Chunhui Huang and Xiaobiao Xu

Int. J. Mol. Sci. 2023, 24(24), 17182; https://doi.org/10.3390/ijms242417182 - 6 Dec 2023

Cited by 4 | Viewed by 1022

Abstract

Ascorbic acid is a potent antioxidant and a crucial nutrient for plants and animals. The accumulation of ascorbic acid in plants is controlled by its biosynthesis, recycling, and degradation. Monodehydroascorbate reductase is deeply involved in the ascorbic acid cycle; however, the mechanism of monodehydroascorbate reductase genes in regulating kiwifruit ascorbic acid accumulation remains unclear. Here, we identified seven monodehydroascorbate reductase genes in the genome of kiwifruit (Actinidia eriantha) and they were designated as AeMDHAR1 to AeMDHAR7, following their genome identifiers. We found that the relative expression level of AeMDHAR3 in fruit continued to decline during development. The over-expression of kiwifruit AeMDHAR3 in tomato plants improved monodehydroascorbate reductase activity, and, unexpectedly, ascorbic acid content decreased significantly in the fruit of the transgenic tomato lines. Ascorbate peroxidase activity also increased significantly in the transgenic lines. In addition, a total of 1781 differentially expressed genes were identified via transcriptomic analysis. Three kinds of ontologies were identified, and 106 KEGG pathways were significantly enriched for these differently expressed genes. Expression verification via quantitative real-time PCR analysis confirmed the reliability of the RNA-seq data. Furthermore, APX3, belonging to the ascorbate and aldarate metabolism pathway, was identified as a key candidate gene that may be primarily responsible for the decrease in ascorbic acid concentration in transgenic tomato fruits. The present study provides novel evidence to support the feedback regulation of ascorbic acid accumulation in the fruit of kiwifruit. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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21 pages, 608 KiB

Open AccessReview

Advancements in Reference Gene Selection for Fruit Trees: A Comprehensive Review

by Shujun Peng, Irfan Ali Sabir, Xinglong Hu, Jiayi Chen and Yonghua Qin

Int. J. Mol. Sci. 2024, 25(2), 1142; https://doi.org/10.3390/ijms25021142 - 17 Jan 2024

Viewed by 1383

Abstract

Real-time quantitative polymerase chain reaction (qRT-PCR) has been widely used in gene expression analyses due to its advantages of sensitivity, accuracy and high throughput. The stability of internal reference genes has progressively emerged as a major factor affecting the precision of qRT-PCR results. However, the stability of the expression of the reference genes needs to be determined further in different cells or organs, physiological and experimental conditions. Methods for evaluating these candidate internal reference genes have also evolved from simple single software evaluation to more reliable and accurate internal reference gene evaluation by combining different software tools in a comprehensive analysis. This study intends to provide a definitive reference for upcoming research that will be conducted on fruit trees. The primary focus of this review is to summarize the research progress in recent years regarding the selection and stability analysis of candidate reference genes for different fruit trees. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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19 pages, 3352 KiB

Open AccessArticle

Physiological, Metabolic, and Transcriptomic Analyses Reveal Mechanisms of Proliferation and Somatic Embryogenesis of Litchi (Litchi chinensis Sonn.) Embryogenic Callus Promoted by D-Arginine Treatment

by Ludan Cao, Guo Wang, Xiuxu Ye, Fang Li, Shujun Wang, Huanling Li, Peng Wang and Jiabao Wang

Int. J. Mol. Sci. 2024, 25(7), 3965; https://doi.org/10.3390/ijms25073965 - 2 Apr 2024

Cited by 1 | Viewed by 1218

Abstract

D-arginine (D-Arg) can promote embryogenic callus (EC) proliferation and increase the rate of somatic embryo induction of litchi (Litchi chinensis Sonn.), yet the mechanism underlying the processes is incompletely understood. To investigate the mechanism, physiological responses of polyamines (PAs) [putrescine (Put), spermidine (Spd), and spermine (Spm)] were investigated for D-Arg-treated litchi EC and enzyme activity related to polyamine metabolism, plant endogenous hormones, and polyamine- and embryogenic-related genes were explored. Results showed that the exogenous addition of D-Arg reduces the activity of diamine oxidase (DAO) and polyamine oxidase (PAO) in EC, reduces the production of H₂O₂, promotes EC proliferation, and increases the (Spd + Spm)/Put ratio to promote somatic embryo induction. Exogenous D-Arg application promoted somatic embryogenesis (SE) by increasing indole-3-acetyl glycine (IAA-Gly), kinetin-9-glucoside (K9G), and dihydrozeatin-7-glucoside (DHZ7G) levels and decreasing trans-zeatin riboside (tZR), N-[(-)-jasmonoyl]-(L)-valine (JA-Val), jasmonic acid (JA), and jasmonoyl-L-isoleucine (Ja-ILE) levels on 18 d, as well as promoting cell division and differentiation. The application of exogenous D-Arg regulated EC proliferation and somatic embryo induction by altering gene expression levels of the WRKY family, AP2/ERF family, C3H family, and C2H2 family. These results indicate that exogenous D-Arg could regulate the proliferation of EC and the SE induction of litchi by changing the biosynthesis of PAs through the alteration of gene expression pattern and endogenous hormone metabolism. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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20 pages, 7008 KiB

Open AccessArticle

Molecular Characteristics and Functional Identification of a Key Alpha-Amylase-Encoding Gene AMY11 in Musa acuminata

by Peiguang Sun, Zhao Zhu, Zhiqiang Jin, Jianghui Xie, Hongxia Miao and Juhua Liu

Int. J. Mol. Sci. 2024, 25(14), 7832; https://doi.org/10.3390/ijms25147832 - 17 Jul 2024

Viewed by 831

Abstract

Alpha-amylase (AMY) plays a significant role in regulating the growth, development, and postharvest quality formation in plants. Nevertheless, little is known about the genome-wide features, expression patterns, subcellular localization, and functional regulation of AMY genes (MaAMYs) in the common starchy banana (Musa acuminata). Twelve MaAMY proteins from the banana genome database were clustered into two groups and contained a conserved catalytic domain. These MaAMYs formed collinear pairs with the AMYs of maize and rice. Three tandem gene pairs were found within the MaAMYs and are indicative of putative gene duplication events. Cis-acting elements of the MaAMY promoters were found to be involved in phytohormone, development, and stress responses. Furthermore, MaAMY02, 08, 09, and 11 were actively expressed during fruit development and ripening. Specifically, MaAMY11 showed the highest expression level at the middle and later stages of banana ripening. Subcellular localization showed that MaAMY02 and 11 were predominately found in the chloroplast, whereas MaAMY08 and 09 were primarily localized in the cytoplasm. Notably, transient attenuation of MaAMY11 expression resulted in an obvious increase in the starch content of banana fruit, while a significant decrease in starch content was confirmed through the transient overexpression of MaAMY11. Together, these results reveal new insights into the structure, evolution, and expression patterns of the MaAMY family, affirming the functional role of MaAMY11 in the starch degradation of banana fruit. Full article

(This article belongs to the Special Issue Molecular Research of Tropical Fruit)

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