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Advances in Research for Fruit Crop Breeding and Genetics 2023

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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 October 2023) | Viewed by 24931

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Special Issue Editor

Dr. Pedro Martínez-Gómez

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CEBAS-CSIC, Centro de Edafología y Biología Aplicada del Segura, Department of Plant Breeding, 30100 Murcia, Spain
Interests: Prunus breeding; marker-assisted selection; integrating genetic; genomic; transcriptomic; proteomic and epigenetic approaches
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Dear Colleagues,

The development of new fruit varieties is a long and tedious process involving crossing the parents with selected traits to generate desired seedling progenies to develop superior cultivars. While breeders’ ability to generate large populations of such progenies is almost unlimited, the management and selection of these seedlings limit the progress of this process. Therefore, molecular studies on the development of marker-assisted selection (MAS) strategies are particularly crucial, especially for fruit species with long juvenile periods, whose character evaluation, including their interaction with the rootstock, is expensive and time-consuming. In addition, most fruit species have been sequenced and their reference genomes are available; this genomic analysis has evidenced high synteny between genomes and transcriptomes. The present post-genomic era has given rise to new features that can be applied to fruit species from a methodological point of view and from a global perspective. Firstly, researchers in this era have incorporated high-throughput sequencing methods for DNA, RNA, proteins and epigenetic events. In addition, from a global perspective, the center of gravity of the molecular processes is focused on the expression of genes and the way in which such expression is regulated, analyzing different omics, including genomics, transcriptomics, proteomics or epigenetic. This global omic perspective will investigated in this Special Issue, which will highlight the main conclusions of this recent development for fruit crop breeding and production.

Dr. Pedro Martínez-Gómez
Guest Editor

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Keywords

fruit
breeding
genetic
genomic
transcriptomic
proteomic
epigenetic

Related Special Issues

Advances in Research on Fruit Crop Breeding and Genetics 3.0 in International Journal of Molecular Sciences (1 article)
Advances in Research for Fruit Crop Breeding and Genetics in International Journal of Molecular Sciences (15 articles)

Published Papers (14 papers)

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20 pages, 2574 KiB

Open AccessArticle

A New One-Tube Reaction Assay for the Universal Determination of Sweet Cherry (Prunus avium L.) Self-(In)Compatible MGST- and S-Alleles Using Capillary Fragment Analysis

by Jana Čmejlová, František Paprštein, Pavol Suran, Lubor Zelený and Radek Čmejla

Int. J. Mol. Sci. 2023, 24(8), 6931; https://doi.org/10.3390/ijms24086931 - 08 Apr 2023

Cited by 1 | Viewed by 1405

Abstract

The sweet cherry plant (Prunus avium L.) is primarily self-incompatible, with so-called S-alleles responsible for the inability of flowers to be pollinated not only by their own pollen grains but also by pollen from other cherries having the same S-alleles. This characteristic has wide-ranging impacts on commercial growing, harvesting, and breeding. However, mutations in S-alleles as well as changes in the expression of M locus-encoded glutathione-S-transferase (MGST) can lead to complete or partial self-compatibility, simplifying orchard management and reducing possible crop losses. Knowledge of S-alleles is important for growers and breeders, but current determination methods are challenging, requiring several PCR runs. Here we present a system for the identification of multiple S-alleles and MGST promoter variants in one-tube PCR, with subsequent fragment analysis on a capillary genetic analyzer. The assay was shown to unequivocally determine three MGST alleles, 14 self-incompatible S-alleles, and all three known self-compatible S-alleles (S3′, S4′, S5′) in 55 combinations tested, and thus it is especially suitable for routine S-allele diagnostics and molecular marker-assisted breeding for self-compatible sweet cherries. In addition, we identified a previously unknown S-allele in the ’Techlovicka´ genotype (S54) and a new variant of the MGST promoter with an 8-bp deletion in the ´Kronio´ cultivar. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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17 pages, 6757 KiB

Open AccessArticle

Genome-Wide Characteristics of GH9B Family Members in Melon and Their Expression Profiles under Exogenous Hormone and Far-Red Light Treatment during the Grafting Healing Process

by Yulei Zhu, Jieying Guo, Fang Wu, Hanqi Yu, Jiahuan Min, Yingtong Zhao and Chuanqiang Xu

Int. J. Mol. Sci. 2023, 24(9), 8258; https://doi.org/10.3390/ijms24098258 - 04 May 2023

Cited by 3 | Viewed by 1271

Abstract

β-1,4-glucanase can not only promote the wound healing of grafted seedlings but can also have a positive effect on a plant’s cell wall construction. As a critical gene of β-1,4-glucanase, GH9B is involved in cell wall remodeling and intercellular adhesion and plays a vital role in grafting healing. However, the GH9B family members have not yet been characterized for melons. In this study, 18 CmGH9Bs were identified from the melon genome, and these CmGH9Bs were located on 15 chromosomes. Our phylogenetic analysis of these CmGH9B genes and GH9B genes from other species divided them into three clusters. The gene structure and conserved functional domains of CmGH9Bs in different populations differed significantly. However, CmGH9Bs responded to cis elements such as low temperature, exogenous hormones, drought, and injury induction. The expression profiles of CmGH9Bs were different. During the graft healing process of the melon scion grafted onto the squash rootstock, both exogenous naphthyl acetic acid (NAA) and far-red light treatment significantly induced the upregulated expression of CmGH9B14 related to the graft healing process. The results provided a technical possibility for managing the graft healing of melon grafted onto squash by regulating CmGH9B14 expression. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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39 pages, 2596 KiB

Open AccessReview

Marker-Assisted Selection in Breeding for Fruit Trait Improvement: A Review

by Gloria De Mori and Guido Cipriani

Int. J. Mol. Sci. 2023, 24(10), 8984; https://doi.org/10.3390/ijms24108984 - 19 May 2023

Cited by 4 | Viewed by 3324

Abstract

Breeding fruit species is time-consuming and expensive. With few exceptions, trees are likely the worst species to work with in terms of genetics and breeding. Most are characterized by large trees, long juvenile periods, and intensive agricultural practice, and environmental variability plays an important role in the heritability evaluations of every single important trait. Although vegetative propagation allows for the production of a significant number of clonal replicates for the evaluation of environmental effects and genotype × environment interactions, the spaces required for plant cultivation and the intensity of work necessary for phenotypic surveys slow down the work of researchers. Fruit breeders are very often interested in fruit traits: size, weight, sugar and acid content, ripening time, fruit storability, and post-harvest practices, among other traits relevant to each individual species. The translation of trait loci and whole-genome sequences into diagnostic genetic markers that are effective and affordable for use by breeders, who must choose genetically superior parents and subsequently choose genetically superior individuals among their progeny, is one of the most difficult tasks still facing tree fruit geneticists. The availability of updated sequencing techniques and powerful software tools offered the opportunity to mine tens of fruit genomes to find out sequence variants potentially useful as molecular markers. This review is devoted to analysing what has been the role of molecular markers in assisting breeders in selection processes, with an emphasis on the fruit traits of the most important fruit crops for which examples of trustworthy molecular markers have been developed, such as the MDo.chr9.4 marker for red skin colour in apples, the CCD4-based marker CPRFC1, and LG3_13.146 marker for flesh colour in peaches, papayas, and cherries, respectively. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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23 pages, 1223 KiB

Open AccessReview

CRISPR/Cas as a Genome-Editing Technique in Fruit Tree Breeding

by Marina Martín-Valmaseda, Sama Rahimi Devin, Germán Ortuño-Hernández, Cristian Pérez-Caselles, Sayyed Mohammad Ehsan Mahdavi, Geza Bujdoso, Juan Alfonso Salazar, Pedro Martínez-Gómez and Nuria Alburquerque

Int. J. Mol. Sci. 2023, 24(23), 16656; https://doi.org/10.3390/ijms242316656 - 23 Nov 2023

Cited by 1 | Viewed by 1913

Abstract

CRISPR (short for “Clustered Regularly Interspaced Short Palindromic Repeats”) is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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21 pages, 15134 KiB

Open AccessArticle

Characterization and Functional Analysis of Chalcone Synthase Genes in Highbush Blueberry (Vaccinium corymbosum)

by Zening Zhang, Pengyan Qu, Siyi Hao, Ruide Li, Yongyan Zhang, Qi Zhao, Pengfei Wen and Chunzhen Cheng

Int. J. Mol. Sci. 2023, 24(18), 13882; https://doi.org/10.3390/ijms241813882 - 09 Sep 2023

Viewed by 1196

Abstract

Chalcone synthase (CHS) is the first key enzyme-catalyzing plant flavonoid biosynthesis. Until now, however, the blueberry CHS gene family has not been systematically characterized and studied. In this study, we identified 22 CHS genes that could be further classified into four subfamilies from the highbush blueberry (Vaccinium corymbosum) genome. This classification was well supported by the high nucleotide and protein sequence similarities and similar gene structure and conserved motifs among VcCHS members from the same subfamily. Gene duplication analysis revealed that the expansion of the blueberry CHS gene family was mainly caused by segmental duplications. Promoter analysis revealed that the promoter regions of VcCHSs contained numerous cis-acting elements responsive to light, phytohormone and stress, along with binding sites for 36 different types of transcription factors. Gene expression analysis revealed that Subfamily I VcCHSs highly expressed in fruits at late ripening stages. Through transient overexpression, we found that three VcCHSs (VcCHS13 from subfamily II; VcCHS8 and VcCHS21 from subfamily I) could significantly enhance the anthocyanin accumulation and up-regulate the expression of flavonoid biosynthetic structural genes in blueberry leaves and apple fruits. Notably, the promoting effect of the Subfamily I member VcCHS21 was the best. The promoter of VcCHS21 contains a G-box (CACGTG) and an E-box sequence, as well as a bHLH binding site. A yeast one hybridization (Y1H) assay revealed that three anthocyanin biosynthesis regulatory bHLHs (VcAN1, VcbHLH1-1 and VcbHLH1-2) could specifically bind to the G-box sequence (CACGTG) in the VcCHS21 promoter, indicating that the expression of VcCHS21 was regulated by bHLHs. Our study will be helpful for understanding the characteristics and functions of blueberry CHSs. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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18 pages, 2532 KiB

Open AccessArticle

CRISPR/Cas9-Mediated Cytosine Base Editing Using an Improved Transformation Procedure in Melon (Cucumis melo L.)

by Hadi Shirazi Parsa, Mohammad Sadegh Sabet, Ahmad Moieni, Abdolali Shojaeiyan, Catherine Dogimont, Adnane Boualem and Abdelhafid Bendahmane

Int. J. Mol. Sci. 2023, 24(13), 11189; https://doi.org/10.3390/ijms241311189 - 07 Jul 2023

Cited by 1 | Viewed by 1817

Abstract

Melon is a recalcitrant plant for stable genetic transformation. Various protocols have been tried to improve melon transformation efficiency; however, it remains significantly low compared to other plants such as tomato. In this study, the primary focus was on the optimization of key parameters during the inoculation and co-culture steps of the genetic transformation protocol. Our results showed that immersing the explants in the inoculation medium for 20 min significantly enhanced transformation efficiency. During the co-culture step, the use of filer paper, 10 mM 2-(N-morpholino)-ethanesulfonic acid (MES), and a temperature of 24 °C significantly enhanced the melon transformation efficiency. Furthermore, the impact of different ethylene inhibitors and absorbers on the transformation efficiency of various melon varieties was explored. Our findings revealed that the use of these compounds led to a significant improvement in the transformation efficiency of the tested melon varieties. Subsequently, using our improved protocol and reporter-gene construct, diploid transgenic melons successfully generated. The efficiency of plant genetic transformation ranged from 3.73 to 4.83%. Expanding the scope of our investigation, the optimized protocol was applied to generate stable gene-edited melon lines using the Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated cytosine base editor and obtained melon lines with editions (C-to-T and C-to-G) in the eukaryotic translation initiation factor 4E, CmeIF4E gene. In conclusion, the optimized melon transformation protocol, along with the utilization of the CRISPR/Cas9-mediated cytosine base editor, provides a reliable framework for functional gene engineering in melon. These advancements hold significant promise for furthering genetic research and facilitating crop improvement in this economically important plant species. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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23 pages, 4798 KiB

Open AccessArticle

Towards Marker-Assisted Breeding for Black Rot Bunch Resistance: Identification of a Major QTL in the Grapevine Cultivar ‘Merzling’

by Paola Bettinelli, Daniela Nicolini, Laura Costantini, Marco Stefanini, Ludger Hausmann and Silvia Vezzulli

Int. J. Mol. Sci. 2023, 24(4), 3568; https://doi.org/10.3390/ijms24043568 - 10 Feb 2023

Cited by 4 | Viewed by 2573

Abstract

Black rot (BR), caused by Guignardia bidwellii, is an emergent fungal disease threatening viticulture and affecting several mildew-tolerant varieties. However, its genetic bases are not fully dissected yet. For this purpose, a segregating population derived from the cross ‘Merzling’ (hybrid, resistant) × ‘Teroldego’ (V. vinifera, susceptible) was evaluated for BR resistance at the shoot and bunch level. The progeny was genotyped with the GrapeReSeq Illumina 20K SNPchip, and 7175 SNPs were combined with 194 SSRs to generate a high-density linkage map of 1677 cM. The QTL analysis based on shoot trials confirmed the previously identified Resistance to Guignardia bidwellii (Rgb)1 locus on chromosome 14, which explained up to 29.2% of the phenotypic variance, reducing the genomic interval from 2.4 to 0.7 Mb. Upstream of Rgb1, this study revealed a new QTL explaining up to 79.9% of the variance for bunch resistance, designated Rgb3. The physical region encompassing the two QTLs does not underlie annotated resistance (R)-genes. The Rgb1 locus resulted enriched in genes belonging to phloem dynamics and mitochondrial proton transfer, while Rgb3 presented a cluster of pathogenesis-related Germin-like protein genes, promoters of the programmed cell death. These outcomes suggest a strong involvement of mitochondrial oxidative burst and phloem occlusion in BR resistance mechanisms and provide new molecular tools for grapevine marker-assisted breeding. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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20 pages, 16459 KiB

Open AccessArticle

Influences of Jujube Witches’ Broom (JWB) Phytoplasma Infection and Oxytetracycline Hydrochloride Treatment on the Gene Expression Profiling in Jujube

by Junqiang Yang, Zhongmei Shen, Pengyan Qu, Rui Yang, Anping Shao, Hao Li, Ailing Zhao and Chunzhen Cheng

Int. J. Mol. Sci. 2023, 24(12), 10313; https://doi.org/10.3390/ijms241210313 - 18 Jun 2023

Cited by 1 | Viewed by 1439

Abstract

Jujube witches’ broom disease (JWB), caused by Candidatus Phytoplasma ziziphi, is the most destructive phytoplasma disease threatening the jujube industry. Tetracycline derivatives treatments have been validated to be capable of recovering jujube trees from phytoplasma infection. In this study, we reported that oxytetracycline hydrochloride (OTC-HCl) trunk injection treatment could recover more than 86% of mild JWB-diseased trees. In order to explore the underlying molecular mechanism, comparative transcriptomic analysis of healthy control (C group), JWB-diseased (D group) and OTC-HCl treated JWB-diseased (T group) jujube leaves was performed. In total, 755 differentially expressed genes (DEGs), including 488 in ‘C vs. D’, 345 in ‘D vs. T’ and 94 in ‘C vs. T’, were identified. Gene enrichment analysis revealed that these DEGs were mainly involved in DNA and RNA metabolisms, signaling, photosynthesis, plant hormone metabolism and transduction, primary and secondary metabolisms, their transportations, etc. Notably, most of the DEGs identified in ‘C vs. D’ displayed adverse change patterns in ‘D vs. T’, suggesting that the expression of these genes was restored after OTC-HCl treatment. Our study revealed the influences of JWB phytoplasma infection and OTC-HCl treatment on gene expression profiling in jujube and would be helpful for understanding the chemotherapy effects of OTC-HCl on JWB-diseased jujube. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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18 pages, 4522 KiB

Open AccessArticle

Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels

by Keliang Lyu, Jiajing Xiao, Shiheng Lyu and Renyi Liu

Int. J. Mol. Sci. 2023, 24(23), 16935; https://doi.org/10.3390/ijms242316935 - 29 Nov 2023

Cited by 1 | Viewed by 814

Abstract

Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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18 pages, 2742 KiB

Open AccessArticle

Scion-to-Rootstock Mobile Transcription Factor CmHY5 Positively Modulates the Nitrate Uptake Capacity of Melon Scion Grafted on Squash Rootstock

by Shu’an Hou, Yulei Zhu, Xiaofang Wu, Ying Xin, Jieying Guo, Fang Wu, Hanqi Yu, Ziqing Sun and Chuanqiang Xu

Int. J. Mol. Sci. 2023, 24(1), 162; https://doi.org/10.3390/ijms24010162 - 22 Dec 2022

Cited by 4 | Viewed by 1737

Abstract

It is generally recognized that the root uptake capacity of grafted plants strongly depends on the rootstocks’ well-developed root system. However, we found that grafted plants showed different nitrate uptake capacities when different varieties of oriental melon scion were grafted onto the same squash rootstock, suggesting that the scion regulated the nitrate uptake capacity of the rootstock root. In this study, we estimated the nitrate uptake capacity of grafted plants with the different oriental melon varieties’ seedlings grafted onto the same squash rootstocks. The results indicated a significant difference in the nitrate uptake rate and activity of two heterologous grafting plants. We also showed a significant difference in CmoNRT2.1 expression in the roots of two grafting combinations and verified the positive regulation of nitrate uptake by CmoNRT2.1 expression. In addition, the two varieties of oriental melon scion had highly significant differences in CmHY5 expression, which was transported to the rootstock and positively induced CmoHY5-1 and CmoHY5-2 expression in the rootstock roots. Meanwhile, CmHY5 could positively regulate CmoNRT2.1 expression in the rootstock roots. Furthermore, CmoHY5-1 and CmoHY5-2 also positively regulated CmoNRT2.1 expression, respectively, and CmoHY5-1 dominated the positive regulation of CmoNRT2.1, while CmHY5 could interact with CmoHY5-1 and CmoHY5-2, respectively, to jointly regulate CmoNRT2.1 expression. The oriental melon scion regulated the nitrate uptake capacity of the melon/squash grafting plant roots, and the higher expression of CmHY5 in the oriental melon scion leaves, the more substantial the nitrate uptake capacity of squash rootstock roots. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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18 pages, 4618 KiB

Open AccessArticle

Integrative Analysis of Metabolomic and Transcriptomic Data Reveals the Mechanism of Color Formation in Corms of Pinellia ternata

by Rong Xu, Ming Luo, Jiawei Xu, Mingxing Wang, Bisheng Huang, Yuhuan Miao and Dahui Liu

Int. J. Mol. Sci. 2023, 24(9), 7990; https://doi.org/10.3390/ijms24097990 - 28 Apr 2023

Viewed by 1860

Abstract

Pinellia ternata (Thunb.) Breit. (P. ternata) is a very important plant that is commonly used in traditional Chinese medicine. Its corms can be used as medicine and function to alleviate cough, headache, and phlegm. The epidermis of P. ternata corms is often light yellow to yellow in color; however, within the range of P. ternata found in JingZhou City in Hubei Province, China, there is a form of P. ternata in which the epidermis of the corm is red. We found that the total flavonoid content of red P. ternata corms is significantly higher than that of yellow P. ternata corms. The objective of this study was to understand the molecular mechanisms behind the difference in epidermal color between the two forms of P. ternata. The results showed that a high content of anthocyanidin was responsible for the red epidermal color in P. ternata, and 15 metabolites, including cyanidin-3-O-rutinoside-5-O-glucoside, cyanidin-3-O-glucoside, and cyanidin-3-O-rutinoside, were screened as potential color markers in P. ternata through metabolomic analysis. Based on an analysis of the transcriptome, seven genes, including PtCHS1, PtCHS2, PtCHI1, PtDFR5, PtANS, PtUPD-GT2, and PtUPD-GT3, were found to have important effects on the biosynthesis of anthocyanins in the P. ternata corm epidermis. Furthermore, two transcription factors (TFs), bHLH1 and bHLH2, may have regulatory functions in the biosynthesis of anthocyanins in red P. ternata corms. Using an integrative analysis of the metabolomic and transcriptomic data, we identified five genes, PtCHI, PtDFR2, PtUPD-GT1, PtUPD-GT2, and PtUPD-GT3, that may play important roles in the presence of the red epidermis color in P. ternata corms. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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19 pages, 1800 KiB

Open AccessReview

Seedlessness Trait and Genome Editing—A Review

by Md Moniruzzaman, Ahmed G. Darwish, Ahmed Ismail, Ashraf El-kereamy, Violeta Tsolova and Islam El-Sharkawy

Int. J. Mol. Sci. 2023, 24(6), 5660; https://doi.org/10.3390/ijms24065660 - 16 Mar 2023

Cited by 2 | Viewed by 2706

Abstract

Parthenocarpy and stenospermocarpy are the two mechanisms underlying the seedless fruit set program. Seedless fruit occurs naturally and can be produced using hormone application, crossbreeding, or ploidy breeding. However, the two types of breeding are time-consuming and sometimes ineffective due to interspecies hybridization barriers or the absence of appropriate parental genotypes to use in the breeding process. The genetic engineering approach provides a better prospect, which can be explored based on an understanding of the genetic causes underlying the seedlessness trait. For instance, CRISPR/Cas is a comprehensive and precise technology. The prerequisite for using the strategy to induce seedlessness is identifying the crucial master gene or transcription factor liable for seed formation/development. In this review, we primarily explored the seedlessness mechanisms and identified the potential candidate genes underlying seed development. We also discussed the CRISPR/Cas-mediated genome editing approaches and their improvements. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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14 pages, 1575 KiB

Open AccessArticle

Optimization of In Vitro Embryo Rescue and Development of a Kompetitive Allele-Specific PCR (KASP) Marker Related to Stenospermocarpic Seedlessness in Grape (Vitis vinifera L.)

by Xiaojun Xi, Benjamin Gutierrez, Qian Zha, Xiangjing Yin, Pengpeng Sun and Aili Jiang

Int. J. Mol. Sci. 2023, 24(24), 17350; https://doi.org/10.3390/ijms242417350 - 11 Dec 2023

Viewed by 661

Abstract

Seedlessness is one of the highest valued agronomic traits in grapes. Embryo rescue in combination with marker-assisted selection have been widely applied in seedless grape breeding due to the advantages of increasing the ratio of seedless progenies and shortening the breeding cycle. However, the large number of deformed seedlings produced during embryo rescue and the lack of fast, efficient, and low-cost markers severely inhibit the process of seedless grape breeding. In this study, a total of eighty-three grape cultivars (51 seedless and 32 seeded) with diverse genetic backgrounds and two populations derived from embryo rescue, including 113 F1 hybrid individuals (60 seedless and 53 seeded), were utilized. We screened suitable media for converting malformed seedlings into normal seedlings, analyzed the association between the SNP in VviAGL11 and seeded/seedless phenotype, and developed a KASP marker related to stenospermocarpic seedlessness. Our results indicated that the transformation rate of 37.8% was obtained with MS medium supplemented with 2.0 mg·L⁻¹ of 6-BA and 0.5 mg·L⁻¹ of IBA. The presence of an A nucleotide allele at position chr18:26889437 was further confirmed to be fully associated with the stenospermocarpic seedlessness phenotype. The developed KASP marker, based on the verified SNP locus in VviAGL11, successfully distinguished the seedless and seeded genotypes with high precision and throughput. The results will contribute to enhancing the efficiency of embryo rescue and facilitate parent selection and early selection of seedless offspring with molecular markers, thereby accelerating the breeding process in seedless table grapes. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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19 pages, 5009 KiB

Open AccessArticle

Genome-Wide Identification and Evolution of the GRF Gene Family and Functional Characterization of PbGRF18 in Pear

by Rongxiang Zhu, Beibei Cao, Manyi Sun, Jun Wu and Jiaming Li

Int. J. Mol. Sci. 2023, 24(19), 14690; https://doi.org/10.3390/ijms241914690 - 28 Sep 2023

Cited by 1 | Viewed by 988

Abstract

Proteins encoded by the G-box regulating factor (GRF, also called 14-3-3) gene family are involved in protein–protein interactions and mediate signaling transduction, which play important roles in plant growth, development, and stress responses. However, there were no detailed investigations of the GRF gene family in pear at present. In this study, we identified 25 GRF family members in the pear genome. Based on a phylogenetic analysis, the 25 GRF genes were clustered into two groups; the ε group and the non-ε group. Analyses of the exon–intron structures and motifs showed that the gene structures were conserved within each of the ε and non-ε groups. Gene duplication analysis indicated that most of the PbGRF gene expansion that occurred in both groups was due to WGD/segmental duplication. Phosphorylation sites analysis showed that the main phosphorylation sites of PbGRF proteins were serine residues. For gene expression, five PbGRF genes (PbGRF7, PbGRF11, PbGRF16, PbGRF21, and PbGRF23) were highly expressed in fruits, and PbGRF18 was highly expressed in all tissues. Further analysis revealed that eight PbGRF genes were significantly differentially expressed after treatment with different sugars; the expression of PbGRF7, PbGRF8, and PbGRF11 significantly increased, implying the involvement of these genes in sugar signaling. In addition, subcellular localization studies showed that the tested GRF proteins localize to the plasma membrane, and transgenic analysis showed that PbGRF18 can increase the sugar content in tomato leaves and fruit. The results of our research establish a foundation for functional determination of PbGRF proteins, and will help to promote a further understanding of the regulatory network in pear fruit development. Full article

(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics 2023)

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