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2 pages, 177 KiB

Open AccessEditorial

Editorial for the Special Issue “Genetic Sight: Plant Traits during Postharvest”

by Shimeles Tilahun

Curr. Issues Mol. Biol. 2023, 45(4), 3515-3516; https://doi.org/10.3390/cimb45040229 - 18 Apr 2023

Viewed by 1209

Abstract

Modern breeding alternatives are less costly and sustainable solutions to increase quality, resistance to biotic and abiotic stresses, and to reduce postharvest losses of crops [...] Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

Research

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14 pages, 3701 KiB

Open AccessArticle

Altering Stomatal Density for Manipulating Transpiration and Photosynthetic Traits in Rice through CRISPR/Cas9 Mutagenesis

by Sakthi Ambothi Rathnasamy, Rohit Kambale, Allimuthu Elangovan, Williams Mohanavel, Priyanka Shanmugavel, Gowtham Ramasamy, Senthil Alagarsamy, Rajavel Marimuthu, Veera Ranjani Rajagopalan, Sudha Manickam, Valarmathi Ramanathan, Raveendran Muthurajan and Geethalakshmi Vellingiri

Curr. Issues Mol. Biol. 2023, 45(5), 3801-3814; https://doi.org/10.3390/cimb45050245 - 30 Apr 2023

Cited by 7 | Viewed by 4481

Abstract

Stomata regulates conductance, transpiration and photosynthetic traits in plants. Increased stomatal density may contribute to enhanced water loss and thereby help improve the transpirational cooling process and mitigate the high temperature-induced yield losses. However, genetic manipulation of stomatal traits through conventional breeding still [...] Read more.

Stomata regulates conductance, transpiration and photosynthetic traits in plants. Increased stomatal density may contribute to enhanced water loss and thereby help improve the transpirational cooling process and mitigate the high temperature-induced yield losses. However, genetic manipulation of stomatal traits through conventional breeding still remains a challenge due to problems involved in phenotyping and the lack of suitable genetic materials. Recent advances in functional genomics in rice identified major effect genes determining stomatal traits, including its number and size. Widespread applications of CRISPR/Cas9 in creating targeted mutations paved the way for fine tuning the stomatal traits for enhancing climate resilience in crops. In the current study, attempts were made to create novel alleles of OsEPF1 (Epidermal Patterning Factor), a negative regulator of stomatal frequency/density in a popular rice variety, ASD 16, using the CRISPR/Cas9 approach. Evaluation of 17 T₀ progenies identified varying mutations (seven multiallelic, seven biallelic and three monoallelic mutations). T₀ mutant lines showed a 3.7–44.3% increase in the stomatal density, and all the mutations were successfully inherited into the T₁ generation. Evaluation of T₁ progenies through sequencing identified three homozygous mutants for one bp insertion. Overall, T₁ plants showed 54–95% increased stomatal density. The homozygous T₁ lines (# E1-1-4, # E1-1-9 and # E1-1-11) showed significant increase in the stomatal conductance (60–65%), photosynthetic rate (14–31%) and the transpiration rate (58–62%) compared to the nontransgenic ASD 16. Results demonstrated that the genetic alterations in OsEPF1 altered the stomatal density, stomatal conductance and photosynthetic efficiency in rice. Further experiments are needed to associate this technology with canopy cooling and high temperature tolerance. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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15 pages, 2650 KiB

Open AccessArticle

Genetic Mapping and QTL Analysis of Fruit Traits in Melon (Cucumis melo L.)

by Haiyong Zhao, Taifeng Zhang, Xiaobing Meng, Jiayan Song, Chen Zhang and Peng Gao

Curr. Issues Mol. Biol. 2023, 45(4), 3419-3433; https://doi.org/10.3390/cimb45040224 - 14 Apr 2023

Cited by 8 | Viewed by 2872

Abstract

Melon (Cucumis melo L.) is an important horticultural cash crop and its quality traits directly affect consumer choice and market price. These traits are controlled by genetic as well as environmental factors. In this study, a quantitative trait locus (QTL) mapping strategy [...] Read more.

Melon (Cucumis melo L.) is an important horticultural cash crop and its quality traits directly affect consumer choice and market price. These traits are controlled by genetic as well as environmental factors. In this study, a quantitative trait locus (QTL) mapping strategy was used to identify the potential genetic loci controlling quality traits of melons (i.e., exocarp and pericarp firmness and soluble solid content) based on newly derived whole-genome single nucleotide polymorphism-based cleaved amplified polymorphic sequence (SNP-CAPS) markers. Specifically, SNPs of two melon varieties, M4-5 and M1-15, as revealed by whole-genome sequencing, were converted to the CAPS markers, which were used to construct a genetic linkage map comprising 12 chromosomes with a total length of 1414.88 cM, in the F₂ population of M4-5 and M1-15. The six identified QTLs included: SSC6.1 and SSC11.1 related to soluble solid content; EF12.1 associated with exocarp firmness; and EPF3.1, EPF3.2 and EPF7.1 related to edible pericarp firmness. These genes were located on five chromosomes (3, 6, 7, 11, and 12) in the flanking regions of the CAPS markers. Moreover, the newly developed CAPS markers will be useful in guiding genetic engineering and molecular breeding in melon. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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24 pages, 6647 KiB

Open AccessArticle

Development and Optimization of Label-Free Quantitative Proteomics under Different Crossing Periods of Bottle Gourd

by Anurag Malik, Virender Singh Mor, Himani Punia, D. S. Duhan, Jayanti Tokas, Axay Bhuker, Mohammed Nasser Alyemeni and Awais Shakoor

Curr. Issues Mol. Biol. 2023, 45(2), 1349-1372; https://doi.org/10.3390/cimb45020088 - 6 Feb 2023

Cited by 3 | Viewed by 2304

Abstract

Bottle gourd, a common vegetable in the human diet, has been valued for its medicinal and energetic properties. In this experiment, the time-resolved analysis of the changes in the proteins’ electrophoretic patterning of the seed development at different crossing periods was studied in [...] Read more.

Bottle gourd, a common vegetable in the human diet, has been valued for its medicinal and energetic properties. In this experiment, the time-resolved analysis of the changes in the proteins’ electrophoretic patterning of the seed development at different crossing periods was studied in bottle gourd using label-free quantitative proteomics. Hybrid HBGH-35 had the highest observed protein levels at the 4th week of the crossing period (F₄) compared to the parental lines, viz. G-2 (M) and Pusa Naveen (F). The crossing period is significantly correlated with grain filling and reserve accumulation. The observed protein expression profile after storage was related to seed maturation and grain filling in bottle gourds. A total of 2517 proteins were identified in differentially treated bottle gourd fruits, and 372 proteins were differentially expressed between different crossing periods. Proteins related to carbohydrate and energy metabolism, anthocyanin biosynthesis, cell stress response, and fruit firmness were characterized and quantified. Some proteins were involved in the development, while others were engaged in desiccation and the early grain-filling stage. F4 was distinguished by an increase in the accumulation of low molecular weight proteins and enzymes such as amylase, a serine protease, and trypsin inhibitors. The seed vigor also followed similar patterns of differential expression of seed storage proteins. Our findings defined a new window during seed production, which showed that at F₄, maximum photosynthetic assimilates accumulated, resulting in an enhanced source–sink relationship and improved seed production. Our study attempts to observe the protein expression profiling pattern under different crossing periods using label-free quantitative proteomics in bottle gourd. It will facilitate future detailed investigation of the protein associated with quality traits and the agronomic importance of bottle gourd through selective breeding programs. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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8 pages, 6341 KiB

Open AccessCommunication

Hidden Pitfalls of Using Onion Pollen in Molecular Research

by Majd Mardini, Aleksey Ermolaev and Ludmila Khrustaleva

Curr. Issues Mol. Biol. 2023, 45(2), 1065-1072; https://doi.org/10.3390/cimb45020070 - 29 Jan 2023

Cited by 2 | Viewed by 1878

Abstract

There is little information on the use of pollen in molecular research, despite the increased interest in genome editing by pollen-mediated transformation. This paper presents an essential toolbox of technical procedures and observations for molecular studies on onion (Allium cepa L.) pollen. [...] Read more.

There is little information on the use of pollen in molecular research, despite the increased interest in genome editing by pollen-mediated transformation. This paper presents an essential toolbox of technical procedures and observations for molecular studies on onion (Allium cepa L.) pollen. PCR is a useful tool as an express method to evaluate editing results before pollination. A direct PCR protocol for pollen suspension has been adapted without needing DNA pre-extraction. We showed that the outer layer of lipids known as pollenkitt is a limiting factor for successful PCR on pollen. A simple pre-washing step of pollen suspension was able to eliminate the pollenkitt and enormously affect the PCR results. Additionally, our pollenkitt study helped us develop a simple and effective pollination method using wetted onion pollen grains. Classical manual pollination usually is conducted by intact pollen without wetting. Most existing methods of the editing system delivery into pollen are carried out in a wet medium with consequent drying before pollination, which adversely affects the viability of pollen. The optimal medium for wet pollination was 12% sucrose water solution. Our method of using wetted pollen grains for pollination might be very beneficial for pollen genetic manipulation. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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14 pages, 1431 KiB

Open AccessArticle

Mapping QTLs for Super-Earliness and Agro-Morphological Traits in RILs Population Derived from Interspecific Crosses between Pisum sativum × P. fulvum

by Hatice Sari, Tuba Eker, Hilal Sule Tosun, Nedim Mutlu, Ibrahim Celik and Cengiz Toker

Curr. Issues Mol. Biol. 2023, 45(1), 663-676; https://doi.org/10.3390/cimb45010044 - 11 Jan 2023

Cited by 6 | Viewed by 2169

Abstract

Earliness in crop plants has a vital role in prevention of heat-induced drought stress and in combating global warming, which is predicted to exacerbate in the near future. Furthermore, earliness may expand production into northern areas or higher altitudes, having relatively shorter growing [...] Read more.

Earliness in crop plants has a vital role in prevention of heat-induced drought stress and in combating global warming, which is predicted to exacerbate in the near future. Furthermore, earliness may expand production into northern areas or higher altitudes, having relatively shorter growing season and may also expand arable lands to meet global food demands. The primary objective of the present study was to investigate quantitative trait loci (QTLs) for super-earliness and important agro-morphological traits in a recombinant inbred line (RIL) population derived from an interspecific cross. A population of 114 RILs developed through single-seed descent from an interspecific cross involving Pisum sativum L. and P. fulvum Sibth. et Sm. was evaluated to identify QTLs for super-earliness and important agro-morphological traits. A genetic map was constructed with 44 SSRs markers representing seven chromosomes with a total length of 262.6 cM. Of the 14 QTLs identified, two were for super-earliness on LG2, one for plant height on LG3, six for number of pods per plant on LG2, LG4, LG5 and LG6, one for number of seeds per pod on LG6, one for pod length on LG4 and three for harvest index on LG3, LG5, and LG6. AA205 and AA372-1 flanking markers for super-earliness QTLs were suggested for marker-assisted selection (MAS) in pea breeding programs due to high heritability of the trait. This is the first study to map QTLs originating from P. sativum and P. fulvum recently identified species with super-earliness character and the markers (AA205 and AA372-1) linked to QTLs were valuable molecular tools for pea breeding. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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21 pages, 5868 KiB

Open AccessArticle

Characterization of Highbush Blueberry (Vaccinium corymbosum L.) Anthocyanin Biosynthesis Related MYBs and Functional Analysis of VcMYB Gene

by Yongyan Zhang, Dingquan Huang, Bin Wang, Xuelian Yang, Huan Wu, Pengyan Qu, Li Yan, Tao Li, Chunzhen Cheng and Dongliang Qiu

Curr. Issues Mol. Biol. 2023, 45(1), 379-399; https://doi.org/10.3390/cimb45010027 - 3 Jan 2023

Cited by 6 | Viewed by 2191

Abstract

As one of the most important transcription factors regulating plant anthocyanin biosynthesis, MYB has attracted great attentions. In this study, we identified fifteen candidate anthocyanin biosynthesis related MYB (ABRM) proteins, including twelve R2R3-MYBs and three 1R-MYBs, from highbush blueberry. The subcellular localization prediction [...] Read more.

As one of the most important transcription factors regulating plant anthocyanin biosynthesis, MYB has attracted great attentions. In this study, we identified fifteen candidate anthocyanin biosynthesis related MYB (ABRM) proteins, including twelve R2R3-MYBs and three 1R-MYBs, from highbush blueberry. The subcellular localization prediction results showed that, with the exception of VcRVE8 (localized in chloroplast and nucleus), all of the blueberry ABRMs were nucleus-localized. The gene structure analysis revealed that the exon numbers of the blueberry ABRM genes varied greatly, ranging between one and eight. There are many light-responsive, phytohormone-responsive, abiotic stress-responsive and plant growth and development related cis-acting elements in the promoters of the blueberry ABRM genes. It is noteworthy that almost all of their promoters contain light-, ABA- and MeJA-responsive elements, which is consistent with the well-established results that anthocyanin accumulation and the expression of MYBs are influenced significantly by many factors, such as light, ABA and JA. The gene expression analysis revealed that VcMYB, VcMYB6, VcMYB23, VcMYBL2 and VcPH4 are expressed abundantly in blueberry fruits, and VcMYB is expressed the highest in the red, purple and blue fruits among all blueberry ABRMs. VcMYB shared high similarity with functionally proven ABRMs from many other plant species. The gene cloning results showed that VcMYB had three variable transcripts, but only the transient overexpression of VcMYB-1 promoted anthocyanin accumulation in the green fruits. Our study can provide a basis for future research on the anthocyanin biosynthesis related MYBs in blueberry. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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17 pages, 3349 KiB

Open AccessArticle

Identification of Candidate Genes Associated with Pulp Color by Transcriptomic Analysis of ‘Huaxiu’ Plum (Prunus salicina Lindl.) during Fruit-Ripening

by Gang Wang, Wenxin Weng, Zhanhui Jia, Jiyu Zhang, Tao Wang and Jiping Xuan

Curr. Issues Mol. Biol. 2022, 44(12), 6368-6384; https://doi.org/10.3390/cimb44120434 - 15 Dec 2022

Cited by 2 | Viewed by 2096

Abstract

The plum (Prunus salicina Lindl.) is one of the traditional and economically important stone fruit trees in China. Anthocyanins are important pigments in plums. However, little is known about the molecular mechanisms underlying anthocyanin accumulation in plum fruits, which has hindered research [...] Read more.

The plum (Prunus salicina Lindl.) is one of the traditional and economically important stone fruit trees in China. Anthocyanins are important pigments in plums. However, little is known about the molecular mechanisms underlying anthocyanin accumulation in plum fruits, which has hindered research on the molecular mechanism of its utilization. Our research shows that the chlorophyll content was gradually decreased and the contents of anthocyanin and flavonoid increased during the coloring process of the pulp in ‘Huaxiu’ plums (P. salicina). Then, the RNA-Seq technique was used to analyze the transcriptome of pulp color changes with three different stages (yellow, orange, and red) in the ‘Huaxiu’ plum (P. salicina). A total of 57,119 unigenes with a mean length of 953 bp were generated, and 61.6% of them were annotated to public databases. The Gene Ontology (GO) database assigned 21,438 unigenes with biological process, cellular components, and molecular function. In addition, 32,146 unigenes were clustered into 25 categories for functional classification by the COG database, and 7595 unigenes were mapped to 128 KEGG pathways by the KEGG pathway database. Of these, 1095 (YS-versus-OS), 4947 (YS-versus-RS), and 3414 (OS-versus-RS) genes were significantly expressed differentially between two coloration stages. The GO and KEGG pathway enrichment analysis revealed that 20 and 1 differentially expressed genes (DEG) are involved in flavonoid biosynthesis and anthocyanin biosynthesis, respectively. Finally, we mainly identified three structural genes as candidate genes. The transcriptome information in this study provide a basis for further studies of pulp colors in plum and contribute to our understanding of the molecular mechanisms underlying anthocyanin biosynthesis in pulp. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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16 pages, 3877 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the Aquaporin Gene Family in Lycium barbarum during Fruit Ripening and Seedling Response to Heat Stress

by Wei He, Mingyu Liu, Xiaoya Qin, Aihua Liang, Yan Chen, Yue Yin, Ken Qin and Zixin Mu

Curr. Issues Mol. Biol. 2022, 44(12), 5933-5948; https://doi.org/10.3390/cimb44120404 - 28 Nov 2022

Cited by 5 | Viewed by 1997

Abstract

Plant–water relations mediated by aquaporins (AQPs) play vital roles in both key plant growth processes and responses to environmental challenges. As a well-known medicinal and edible plant, the harsh natural growth habitat endows Lycium plants with ideal materials for stress biology research. However, [...] Read more.

Plant–water relations mediated by aquaporins (AQPs) play vital roles in both key plant growth processes and responses to environmental challenges. As a well-known medicinal and edible plant, the harsh natural growth habitat endows Lycium plants with ideal materials for stress biology research. However, the details of their molecular switch for water transport remain unclear. In the present work, we first identified and characterized AQP family genes from Lycium (L.) barbarum at the genome scale and conducted systemic bioinformatics and expression analyses. The results showed that there were 38 Lycium barbarum AQPs (LbAQPs) in L. barbarum, which were classified into four subfamilies, including 17 LbPIP, 9 LbTIP, 10 LbNIP, and 2 LbXIP. Their encoded genes were unevenly distributed on all 12 chromosomes, except chromosome 10. Three of these genes encoded truncated proteins and three genes underwent clear gene duplication events. Cis-acting element analysis indicated that the expression of LbAQPs may be mainly regulated by biotic/abiotic stress, phytohormones and light. The qRT-PCR assay indicated that this family of genes presented a clear tissue-specific expression pattern, in which most of the genes had maximal transcript levels in roots, stems, and leaves, while there were relatively lower levels in flowers and fruits. Most of the LbAQP genes were downregulated during L. barbarum fruit ripening and presented a negative correlation with the fruit relative water content (RWC). Most of their transcripts presented a quick and sharp upregulation response to heat stress following exposure of the 2-month-old seedlings to a 42 °C temperature for 0, 1, 3, 12, or 24 h. Our results proposed that LbAQPs were involved in L. barbarum key development events and abiotic stress responses, which may lay a foundation for further studying the molecular mechanism of the water relationship of Lycium plants, especially in harsh environments. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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13 pages, 1357 KiB

Open AccessArticle

Genetic Relationship of Brassicaceae Hybrids with Various Resistance to Blackleg Is Disclosed by the Use of Molecular Markers

by Justyna Szwarc, Janetta Niemann, Joanna Kaczmarek, Jan Bocianowski and Dorota Weigt

Curr. Issues Mol. Biol. 2022, 44(9), 4290-4302; https://doi.org/10.3390/cimb44090295 - 17 Sep 2022

Cited by 2 | Viewed by 2071

Abstract

Brassica napus is an important oil source. Its narrow gene pool can be widened by interspecific hybridization with the Brassicaceae species. One of the agronomically important traits, that can be transferred through the hybridization, is the resistance to blackleg, a dangerous disease mainly [...] Read more.

Brassica napus is an important oil source. Its narrow gene pool can be widened by interspecific hybridization with the Brassicaceae species. One of the agronomically important traits, that can be transferred through the hybridization, is the resistance to blackleg, a dangerous disease mainly caused by Leptosphaeria maculans. Hybrid individuals can be analyzed with various molecular markers, including Simple Sequence Repeats (SSR). We investigated the genetic similarity of 32 Brassicaceae hybrids and 19 parental components using SSR markers to reveal their genetic relationship. Furthermore, we compared the field resistance to blackleg of the interspecific progenies. The tested set of 15 SSR markers proved to be useful in revealing the genetic distances in the Brassicaceae hybrids and species. However, genetic similarity of the studied hybrids could not be correlated with the level of field resistance to L. maculans. Moreover, our studies confirmed the usefulness of the Brassicaceae hybrids in terms of blackleg management. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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11 pages, 3190 KiB

Open AccessArticle

Characterizations of a Class-I BASIC PENTACYSTEINE Gene Reveal Conserved Roles in the Transcriptional Repression of Genes Involved in Seed Development

by Xianjin Ma, Yifan Yu, Zhikang Hu, Hu Huang, Sijia Li and Hengfu Yin

Curr. Issues Mol. Biol. 2022, 44(9), 4059-4069; https://doi.org/10.3390/cimb44090278 - 7 Sep 2022

Cited by 4 | Viewed by 2440

Abstract

The developmental regulation of flower organs involves the spatio-temporal regulation of floral homeotic genes. BASIC PENTACYSTEINE genes are plant-specific transcription factors that is involved in many aspects of plant development through gene transcriptional regulation. Although studies have shown that the BPC genes are [...] Read more.

The developmental regulation of flower organs involves the spatio-temporal regulation of floral homeotic genes. BASIC PENTACYSTEINE genes are plant-specific transcription factors that is involved in many aspects of plant development through gene transcriptional regulation. Although studies have shown that the BPC genes are involved in the developmental regulation of flower organs, little is known about their role in the formation of double-flower due. Here we characterized a Class I BPC gene (CjBPC1) from an ornamental flower—Camellia japonica. We showed that CjBPC1 is highly expressed in the central whorls of flowers in both single and doubled varieties. Overexpression of CjBPC1 in Arabidopsis thaliana caused severe defects in siliques and seeds. We found that genes involved in ovule and seed development, including SEEDSTICK, LEAFY COTYLEDON2, ABSCISIC ACID INSENSITIVE 3 and FUSCA3, were significantly down-regulated in transgenic lines. We showed that the histone 3 lysine 27 methylation levels of these downstream genes were enhanced in the transgenic plants, indicating conserved roles of CjBPC1 in recruiting the Polycomb Repression Complex for gene suppression. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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13 pages, 15933 KiB

Open AccessArticle

Genome-Wide Identification of DUF26 Domain-Containing Genes in Dongxiang Wild Rice and Analysis of Their Expression Responses under Submergence

by Cheng Huang, Dianwen Wang, Hongping Chen, Wei Deng, Dazhou Chen, Ping Chen and Jilin Wang

Curr. Issues Mol. Biol. 2022, 44(8), 3351-3363; https://doi.org/10.3390/cimb44080231 - 27 Jul 2022

Cited by 4 | Viewed by 2223

Abstract

The DUF26 domain-containing protein is an extracellular structural protein, which plays an important role in signal transduction. Dongxiang wild rice (Oryza rufipogon Griff.) is the northern-most common wild rice in China. Using domain analysis, 85 DUF26 domain-containing genes were identified in Dongxiang [...] Read more.

The DUF26 domain-containing protein is an extracellular structural protein, which plays an important role in signal transduction. Dongxiang wild rice (Oryza rufipogon Griff.) is the northern-most common wild rice in China. Using domain analysis, 85 DUF26 domain-containing genes were identified in Dongxiang wild rice (DXWR) and further divided into four categories. The DUF26 domain-containing genes were unevenly distributed on chromosomes, and there were 18 pairs of tandem repeats. Gene sequence analysis showed that there were significant differences in the gene structure and motif distribution of the DUF26 domain in different categories. Motifs 3, 8, 9, 13, 14, 16, and 18 were highly conserved in all categories. It was also found that there were eight plasmodesmata localization proteins (PDLPs) with a unique motif 19. Collinearity analysis showed that DXWR had a large number of orthologous genes with wheat, maize, sorghum and zizania, of which 17 DUF26 domain-containing genes were conserved in five gramineous crops. Under the stress of anaerobic germination and seedling submergence treatment, 33 DUF26 domain-containing genes were differentially expressed in varying degrees. Further correlation analysis with the expression of known submergence tolerance genes showed that these DUF26 domain-containing genes may jointly regulate the submergence tolerance process with these known submergence tolerance genes in DXWR. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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21 pages, 5735 KiB

Open AccessArticle

Comparative Transcriptome Analysis of Softening and Ripening-Related Genes in Kiwifruit Cultivars Treated with Ethylene

by Han Ryul Choi, Min Woo Baek, Cheon Soon Jeong and Shimeles Tilahun

Curr. Issues Mol. Biol. 2022, 44(6), 2593-2613; https://doi.org/10.3390/cimb44060177 - 2 Jun 2022

Cited by 7 | Viewed by 2595

Abstract

This work presents the transcriptome analysis of green ‘Hayward’ (Actinidia deliciosa) and gold ‘Haegeum’ (Actinidia chinensis) kiwifruit cultivars after treatment with ethylene for three days at 25 °C. Illumina high-throughput sequencing platform was used to sequence total mRNAs and [...] Read more.

This work presents the transcriptome analysis of green ‘Hayward’ (Actinidia deliciosa) and gold ‘Haegeum’ (Actinidia chinensis) kiwifruit cultivars after treatment with ethylene for three days at 25 °C. Illumina high-throughput sequencing platform was used to sequence total mRNAs and the transcriptome gene set was constructed by de novo assembly. A total of 1287 and 1724 unigenes were differentially expressed during the comparison of ethylene treatment with control in green ‘Hayward’ and gold ‘Haegeum’, respectively. From the differentially expressed unigenes, 594 and 906 were upregulated, and 693 and 818 were downregulated in the green and gold kiwifruit cultivars, respectively, when treated with ethylene. We also identified a list of genes that were expressed commonly and exclusively in the green and gold kiwifruit cultivars treated with ethylene. Several genes were expressed differentially during the ripening of kiwifruits, and their cumulative effect brought about the softening- and ripening-related changes. This work also identified and categorized genes related to softening and other changes during ripening. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) identified in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR) to validate the reliability of the expression profiles obtained from RNA-Seq. The data obtained from the present study will add to the information available on the molecular mechanisms of the effects of ethylene during the ripening of kiwifruits. This study will also provide resources for further studies of the genes related to ripening, helping kiwifruit breeders and postharvest technologists to improve ripening quality. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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Review

Jump to: Editorial, Research

25 pages, 2386 KiB

Open AccessReview

Advances in Research on the Regulation of Floral Development by CYC-like Genes

by Yuhong Chai, Hua Liu, Wendan Chen, Chenghu Guo, Haixia Chen, Xi Cheng, Dongliang Chen, Chang Luo, Xiumei Zhou and Conglin Huang

Curr. Issues Mol. Biol. 2023, 45(3), 2035-2059; https://doi.org/10.3390/cimb45030131 - 2 Mar 2023

Cited by 8 | Viewed by 3148

Abstract

CYCLOIDEA (CYC)-like genes belong to the TCP transcription factor family and play important roles associated with flower development. The CYC-like genes in the CYC1, CYC2, and CYC3 clades resulted from gene duplication events. The CYC2 clade includes the largest number [...] Read more.

CYCLOIDEA (CYC)-like genes belong to the TCP transcription factor family and play important roles associated with flower development. The CYC-like genes in the CYC1, CYC2, and CYC3 clades resulted from gene duplication events. The CYC2 clade includes the largest number of members that are crucial regulators of floral symmetry. To date, studies on CYC-like genes have mainly focused on plants with actinomorphic and zygomorphic flowers, including Fabaceae, Asteraceae, Scrophulariaceae, and Gesneriaceae species and the effects of CYC-like gene duplication events and diverse spatiotemporal expression patterns on flower development. The CYC-like genes generally affect petal morphological characteristics and stamen development, as well as stem and leaf growth, flower differentiation and development, and branching in most angiosperms. As the relevant research scope has expanded, studies have increasingly focused on the molecular mechanisms regulating CYC-like genes with different functions related to flower development and the phylogenetic relationships among these genes. We summarize the status of research on the CYC-like genes in angiosperms, such as the limited research conducted on CYC1 and CYC3 clade members, the necessity to functionally characterize the CYC-like genes in more plant groups, the need for investigation of the regulatory elements upstream of CYC-like genes, and exploration of the phylogenetic relationships and expression of CYC-like genes with new techniques and methods. This review provides theoretical guidance and ideas for future research on CYC-like genes. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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34 pages, 1930 KiB

Open AccessReview

OMICS in Fodder Crops: Applications, Challenges, and Prospects

by Pawan Kumar, Jagmohan Singh, Gurleen Kaur, Paul Motunrayo Adunola, Anju Biswas, Sumandeep Bazzer, Harpreet Kaur, Ishveen Kaur, Harpreet Kaur, Karansher Singh Sandhu, Shailaja Vemula, Balwinder Kaur, Varsha Singh and Te Ming Tseng

Curr. Issues Mol. Biol. 2022, 44(11), 5440-5473; https://doi.org/10.3390/cimb44110369 - 3 Nov 2022

Cited by 8 | Viewed by 5169

Abstract

Biomass yield and quality are the primary targets in forage crop improvement programs worldwide. Low-quality fodder reduces the quality of dairy products and affects cattle’s health. In multipurpose crops, such as maize, sorghum, cowpea, alfalfa, and oat, a plethora of morphological and biochemical/nutritional [...] Read more.

Biomass yield and quality are the primary targets in forage crop improvement programs worldwide. Low-quality fodder reduces the quality of dairy products and affects cattle’s health. In multipurpose crops, such as maize, sorghum, cowpea, alfalfa, and oat, a plethora of morphological and biochemical/nutritional quality studies have been conducted. However, the overall growth in fodder quality improvement is not on par with cereals or major food crops. The use of advanced technologies, such as multi-omics, has increased crop improvement programs manyfold. Traits such as stay-green, the number of tillers per plant, total biomass, and tolerance to biotic and/or abiotic stresses can be targeted in fodder crop improvement programs. Omic technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, provide an efficient way to develop better cultivars. There is an abundance of scope for fodder quality improvement by improving the forage nutrition quality, edible quality, and digestibility. The present review includes a brief description of the established omics technologies for five major fodder crops, i.e., sorghum, cowpea, maize, oats, and alfalfa. Additionally, current improvements and future perspectives have been highlighted. Full article

(This article belongs to the Special Issue Genetic Sight: Plant Traits during Postharvest)

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