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Advances in Research for Fruit Crop Breeding and Genetics

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 December 2022) | Viewed by 29302

Special Issue Editor

Dr. Pedro Martínez-Gómez

E-Mail Website
Guest Editor
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
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

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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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • fruit
  • breeding
  • genetic
  • genomic
  • transcriptomic
  • proteomic
  • epigenetic

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Published Papers (15 papers)

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Research

18 pages, 1622 KiB  
Article
S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence
by Afif Hedhly, María Engracia Guerra, Jerome Grimplet and Javier Rodrigo
Int. J. Mol. Sci. 2023, 24(4), 3932; https://doi.org/10.3390/ijms24043932 - 15 Feb 2023
Viewed by 1426
Abstract
Self-incompatibility in Prunus species is governed by a single locus consisting of two highly multi-allelic and tightly linked genes, one coding for an F-box protein—i.e., SFB in Prunus- controlling the pollen specificity and one coding for an S-RNase gene controlling the pistil [...] Read more.
Self-incompatibility in Prunus species is governed by a single locus consisting of two highly multi-allelic and tightly linked genes, one coding for an F-box protein—i.e., SFB in Prunus- controlling the pollen specificity and one coding for an S-RNase gene controlling the pistil specificity. Genotyping the allelic combination in a fruit tree species is an essential procedure both for cross-based breeding and for establishing pollination requirements. Gel-based PCR techniques using primer pairs designed from conserved regions and spanning polymorphic intronic regions are traditionally used for this task. However, with the great advance of massive sequencing techniques and the lowering of sequencing costs, new genotyping-by-sequencing procedures are emerging. The alignment of resequenced individuals to reference genomes, commonly used for polymorphism detection, yields little or no coverage in the S-locus region due to high polymorphism between different alleles within the same species, and cannot be used for this purpose. Using the available sequences of Japanese plum S-loci concatenated in a rosary-like structure as synthetic reference sequence, we describe a procedure to accurately genotype resequenced individuals that allowed the analysis of the S-genotype in 88 Japanese plum cultivars, 74 of them are reported for the first time. In addition to unraveling two new S-alleles from published reference genomes, we identified at least two S-alleles in 74 cultivars. According to their S-allele composition, they were assigned to 22 incompatibility groups, including nine new incompatibility groups reported here for the first time (XXVII-XXXV). Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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13 pages, 4386 KiB  
Article
Comparative Transcriptomic Analysis of Inarching Invigorating Rootstock onto Incompatible Grafts in Citrus
by Wen He, Rui Xie, Liang Luo, Jiufeng Chai, Hao Wang, Yan Wang, Qing Chen, Zhiwei Wu, Shaofeng Yang, Mengyao Li, Yuanxiu Lin, Yunting Zhang, Ya Luo, Yong Zhang, Haoru Tang, Frederick G. Gmitter, Jr. and Xiaorong Wang
Int. J. Mol. Sci. 2022, 23(23), 14523; https://doi.org/10.3390/ijms232314523 - 22 Nov 2022
Cited by 1 | Viewed by 1597
Abstract
Grafting is a technique that is widely used in citrus production. Graft incompatibility often occurs in the orchard. Inarching can effectively improve the vigor of incompatible grafts, but its mechanism remains poorly understood. Our previous studies investigated the scion—rootstock interaction of citrus and [...] Read more.
Grafting is a technique that is widely used in citrus production. Graft incompatibility often occurs in the orchard. Inarching can effectively improve the vigor of incompatible grafts, but its mechanism remains poorly understood. Our previous studies investigated the scion—rootstock interaction of citrus and highlighted the role of hormonal balance and genes in abscisic acid biosynthesis regulation. To further elucidate the mechanism of inarched grafts rejuvenation, Hm/Pt combination (Citrus maxima (Burm.) Merrill cv. ‘Hongmian miyou’ grafted onto Poncirus trifoliata) were inarched with ‘Pujiang Xiangcheng’ (a novel citrus rootstock cultivar recently selected from wild Citrus junos populations), and comprehensive analysis was performed to compare the inarched grafts and controls. Compared with incompatible grafts, the results revealed that inarching could recover the leaf metabolism balance, including reducing starch content, increasing chlorophyll content and restoring the cell structure. Additionally, our results corroborated that hormonal balance and hormone-related genes played a central role in inarching compatibility. Furthermore, the roles of Hsf4, ERF1, NCED3 and PYL were highlighted, and a model for explaining inarched grafts recovery invigoration was proposed. This study shed light on the mechanism of inarching regulation tree vigor and offered deep insights into the scion—rootstock interaction in citrus. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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17 pages, 4172 KiB  
Article
Genome-Wide Association and Expression Analysis of the Lipoxygenase Gene Family in Passiflora edulis Revealing PeLOX4 Might Be Involved in Fruit Ripeness and Ester Formation
by Dongmei Huang, Funing Ma, Bin Wu, Wenhui Lv, Yi Xu, Wenting Xing, Di Chen, Bingqiang Xu and Shun Song
Int. J. Mol. Sci. 2022, 23(20), 12496; https://doi.org/10.3390/ijms232012496 - 18 Oct 2022
Cited by 11 | Viewed by 2457
Abstract
Aroma is an important factor in fruit quality. Passiflora edulis (passion fruit) is popular among consumers because of its rich flavor and nutritional value. Esters are the main components of the volatile aroma of passion fruit. Lipoxygenase (LOX), as the first key enzyme [...] Read more.
Aroma is an important factor in fruit quality. Passiflora edulis (passion fruit) is popular among consumers because of its rich flavor and nutritional value. Esters are the main components of the volatile aroma of passion fruit. Lipoxygenase (LOX), as the first key enzyme upstream of esters, may play an important role in the formation of passion fruit aroma. In this study, a total of 12 passion fruit LOX (PeLOX) members were screened out based on the Passiflora edulis genome database, which were distributed unevenly on 6 chromosomes, all containing the highly conserved lipoxygenase domain and some containing the PLAT domain. The gene structure, evolutionary analysis and cis-acting elements of the family members were predicted in this study. Transcriptome analysis showed that 12 PeLOX genes had different degrees of response to different abiotic stresses (drought stress, salt stress, cold stress, and high temperature). PeLOX1, PeLOX2, PeLOX7, PeLOX11, and PeLOX12 responded significantly to various abiotic stresses, while PeLOX8 and PeLOX9 had little change in expression in all stresses. Quantitative real-time PCR (qRT-PCR) in six tissues revealed that the 12 PeLOX genes exhibited tissue expression specificity, and the relative expression of most genes were particularly high in the roots, stems, and fruits. Focusing on passion fruit ripening and ester synthesis, the transcriptomic analysis showed that with the increase in fruit development and fruit maturity, the expression levels of PeLOX1, PeLOX9, PeLOX11, and PeLOX12 showed downregulated expression, while PeLOX2 and PeLOX4 showed upregulated expression. In particular, the upregulation trend of PeLOX4 was the most obvious, and the qRT-PCR results were consistent with the transcriptome result. Pearson correlation analysis showed that with the development and ripening of fruit, the expression level of PeLOX4, LOX enzyme activity and total ester content all showed an increasing trend, in particular during the period when the peel was red and shrank (from T2 to T3 stage), the esters’ contents increased by 37.4 times; the highest expression levels were all in the T3 period. The results indicated that PeLOX4 may be a candidate gene involved in fruit ripeness and the formation of volatile aroma compounds, with the increase in fruit ripening, the expression level of PeLOX4 increased and the LOX enzyme activity increased accordingly, thereby promoting the synthesis of volatile esters in fruit pulp. Our discovery lays the foundation for the functional study of LOX in passion fruit. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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15 pages, 8724 KiB  
Article
Importance of FaWRKY71 in Strawberry (Fragaria × ananassa) Fruit Ripening
by Maolan Yue, Leiyu Jiang, Nating Zhang, Lianxi Zhang, Yongqiang Liu, Yan Wang, Mengyao Li, Yuanxiu Lin, Yunting Zhang, Yong Zhang, Ya Luo, Xiaorong Wang, Qing Chen and Haoru Tang
Int. J. Mol. Sci. 2022, 23(20), 12483; https://doi.org/10.3390/ijms232012483 - 18 Oct 2022
Cited by 16 | Viewed by 1850
Abstract
WRKY transcription factors play a nonnegligible role in plant growth and development, but little is known about the involvement of WRKY transcription factors in the regulation of fruit ripening. In this study, FaWRKY71 was identified to be closely related to fruit maturation in [...] Read more.
WRKY transcription factors play a nonnegligible role in plant growth and development, but little is known about the involvement of WRKY transcription factors in the regulation of fruit ripening. In this study, FaWRKY71 was identified to be closely related to fruit maturation in octoploid strawberry. FaWRKY71 protein localized in the nucleus and responded to cold, salt, low phosphate, ABA, and light quality in strawberry seedlings. The temporal and spatial pattern expression analysis indicated that FaWRKY71 was expressed in all the detected tissues, especially in the full red fruits. In addition, FaWRKY71 gave rise to the accumulation of anthocyanin content by promoting the expression of structural genes FaF3’H, FaLAR, FaANR, and transport factors FaTT19 and FaTT12 in the flavonoid pathway, and softening the texture of strawberry via up-regulating the abundance of FaPG19 and FaPG21. Furthermore, FaWRKY71 was a positive regulator that mediated resistance against reactive oxygen species by enhancing the enzyme activities of SOD, POD, and CAT, reducing the amount of MDA. Altogether, this study provides new and comprehensive insight into the regulatory mechanisms facilitating fruit ripening in strawberry. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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16 pages, 3309 KiB  
Article
Genome-Wide Identification and Characterization of Banana Ca2+-ATPase Genes and Expression Analysis under Different Concentrations of Ca2+ Treatments
by Ronghui Ma, Na Tian, Jiashui Wang, Minlei Fan, Bin Wang, Pengyan Qu, Shiyao Xu, Yanbing Xu, Chunzhen Cheng and Peitao Lü
Int. J. Mol. Sci. 2022, 23(19), 11914; https://doi.org/10.3390/ijms231911914 - 07 Oct 2022
Cited by 2 | Viewed by 1603
Abstract
Ca2+-ATPases have been confirmed to play very important roles in plant growth and development and in stress responses. However, studies on banana (Musa acuminata) Ca2+-ATPases are very limited. In this study, we identified 18 Ca [...] Read more.
Ca2+-ATPases have been confirmed to play very important roles in plant growth and development and in stress responses. However, studies on banana (Musa acuminata) Ca2+-ATPases are very limited. In this study, we identified 18 Ca2+-ATPase genes from banana, including 6 P-IIA or ER (Endoplasmic Reticulum) type Ca2+-ATPases (MaEACs) and 12 P-IIB or Auto-Inhibited Ca2+-ATPases (MaACAs). The MaEACs and MaACAs could be further classified into two and three subfamilies, respectively. This classification is well supported by their gene structures, which are encoded by protein motif distributions. The banana Ca2+-ATPases were all predicted to be plasma membrane-located. The promoter regions of banana Ca2+-ATPases contain many cis-acting elements and transcription factor binding sites (TFBS). A gene expression analysis showed that banana Ca2+-ATPases were differentially expressed in different organs. By investigating their expression patterns in banana roots under different concentrations of Ca2+ treatments, we found that most banana Ca2+-ATPase members were highly expressed under 4 mM and 2 mM Ca2+ treatments, but their expression decreased under 1 mM and 0 mM Ca2+ treatments, suggesting that their downregulation might be closely related to reduced Ca accumulation and retarded growth under low Ca2+ and Ca2+ deficiency conditions. Our study will contribute to the understanding of the roles of Ca2+-ATPases in banana growth and Ca management. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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15 pages, 4204 KiB  
Article
Characterization of the ABC Transporter G Subfamily in Pomegranate and Function Analysis of PgrABCG14
by Qing Yu, Jiyu Li, Gaihua Qin, Chunyan Liu, Zhen Cao, Botao Jia, Yiliu Xu, Guixiang Li, Yuan Yang, Ying Su and Huping Zhang
Int. J. Mol. Sci. 2022, 23(19), 11661; https://doi.org/10.3390/ijms231911661 - 01 Oct 2022
Cited by 3 | Viewed by 1899
Abstract
ATP-binding cassette subfamily G (ABCG) proteins play important roles in plant growth and development by transporting metabolites across cell membranes. To date, the genetic characteristics and potential functions of pomegranate ABCG proteins (PgrABCGs) have remained largely unknown. In this study, we found that [...] Read more.
ATP-binding cassette subfamily G (ABCG) proteins play important roles in plant growth and development by transporting metabolites across cell membranes. To date, the genetic characteristics and potential functions of pomegranate ABCG proteins (PgrABCGs) have remained largely unknown. In this study, we found that 47 PgrABCGs were divided into five groups according to a phylogenetic analysis; groups I, II, III, and IV members are half-size proteins, and group V members are full-size proteins. PgrABCG14, PgrABCG21, and PgrABCG47 were highly expressed in the inner seed coat but had very low expression levels in the outer seed coat, and the expression levels of these three PgrABCG genes in the inner seed coats of hard-seeded pomegranate ‘Dabenzi’ were higher than those of soft-seeded pomegranate ‘Tunisia’. In addition, the expression of these three PgrABCG genes was highly correlated with the expression of genes involved in lignin biosynthesis and hormone signaling pathways. The evolution of PgrABCG14 presents a highly similar trend to the origin and evolution of lignin biosynthesis during land plant evolution. Ectopic expression of PgrABCG14 in Arabidopsis promoted plant growth and lignin accumulation compared to wild type plants; meanwhile, the expression levels of lignin biosynthesis-related genes (CAD5, C4H, and Prx71) and cytokinin response marker genes (ARR5 and ARR15) were significantly upregulated in transgenic plants, which suggests the potential role of PgrABCG14 in promoting plant growth and lignin accumulation. Taken together, these findings not only provide insight into the characteristics and evolution of PgrABCGs, but also shed a light on the potential functions of PgrABCGs in seed hardness development. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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19 pages, 2787 KiB  
Article
Photosynthetic Efficiency and Glyco-Metabolism Changes in Artificial Triploid Loquats Contribute to Heterosis Manifestation
by Lingli Wang, Meiyan Tu, Jing Li, Shuxia Sun, Haiyan Song, Zihong Xu, Dong Chen and Guolu Liang
Int. J. Mol. Sci. 2022, 23(19), 11337; https://doi.org/10.3390/ijms231911337 - 26 Sep 2022
Cited by 2 | Viewed by 1320
Abstract
Previous studies indicated that extensive genetic variations could be generated due to polyploidy, which is considered to be closely associated with the manifestation of polyploid heterosis. Our previous studies confirmed that triploid loquats demonstrated significant heterosis, other than the ploidy effect, but the [...] Read more.
Previous studies indicated that extensive genetic variations could be generated due to polyploidy, which is considered to be closely associated with the manifestation of polyploid heterosis. Our previous studies confirmed that triploid loquats demonstrated significant heterosis, other than the ploidy effect, but the underlying mechanisms are largely unknown. This study aimed to overcome the narrow genetic distance of loquats, increase the genetic variation level of triploid loquats, and systematically illuminate the heterosis mechanisms of triploid loquats derived from two cross combinations. Here, inter-simple sequence repeats (ISSRs) and simple sequence repeats (SSRs) were adopted for evaluating the genetic diversity, and transcriptome sequencing (RNA-Seq) was performed to investigate gene expression as well as pathway changes in the triploids. We found that extensive genetic variations were produced during the formation of triploid loquats. The polymorphism ratios of ISSRs and SSRs were 43.75% and 19.32%, respectively, and almost all their markers had a PIC value higher than 0.5, suggesting that both ISSRs and SSRs could work well in loquat assisted breeding. Furthermore, our results revealed that by broadening the genetic distance between the parents, genetic variations in triploids could be promoted. Additionally, RNA-Seq results suggested that numerous genes differentially expressed between the triploids and parents were screened out. Moreover, KEGG analyses revealed that “photosynthetic efficiency” and “glyco-metabolism” were significantly changed in triploid loquats compared with the parents, which was consistent with the results of physiological indicator analyses, leaf micro-structure observations, and qRT-PCR validation. Collectively, our results suggested that extensive genetic variations occurred in the triploids and that the changes in the “photosynthetic efficiency” as well as “glyco-metabolism” of triploids might have further resulted in heterosis manifestation in the triploid loquats. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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25 pages, 3457 KiB  
Article
Whole Transcriptome Analyses of Apricots and Japanese Plum Fruits after 1-MCP (Ethylene-Inhibitor) and Ethrel (Ethylene-Precursor) Treatments Reveal New Insights into the Physiology of the Ripening Process
by Juan A. Salazar, David Ruiz, Patricio Zapata, Pedro J. Martínez-García and Pedro Martínez-Gómez
Int. J. Mol. Sci. 2022, 23(19), 11045; https://doi.org/10.3390/ijms231911045 - 20 Sep 2022
Cited by 8 | Viewed by 2011
Abstract
The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after [...] Read more.
The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, ‘Goldrich’ and ‘Santa Rosa’. KEEG and protein–protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in ‘Goldrich’ and ‘Santa Rosa’, respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in ‘Goldrich’ and ‘Santa Rosa’, respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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16 pages, 14960 KiB  
Article
Genome-Wide Analysis of the ERF Family and Identification of Potential Genes Involved in Fruit Ripening in Octoploid Strawberry
by Yunting Zhang, Chenhui Guo, Meiyi Deng, Shanlin Li, Yingying Chen, Xianjie Gu, Guohao Tang, Yuanxiu Lin, Yan Wang, Wen He, Mengyao Li, Yong Zhang, Ya Luo, Xiaorong Wang, Qing Chen and Haoru Tang
Int. J. Mol. Sci. 2022, 23(18), 10550; https://doi.org/10.3390/ijms231810550 - 11 Sep 2022
Cited by 6 | Viewed by 2221
Abstract
Ethylene response factors (ERFs) belonging to the APETALA2/ERF superfamily acted at the end of the ethylene signaling pathway, and they were found to play important roles in plant growth and development. However, the information of ERF genes in strawberry and their involvement in [...] Read more.
Ethylene response factors (ERFs) belonging to the APETALA2/ERF superfamily acted at the end of the ethylene signaling pathway, and they were found to play important roles in plant growth and development. However, the information of ERF genes in strawberry and their involvement in fruit ripening have been limited. Here, a total of 235 ERF members were identified from 426 AP2/ERF genes at octoploid strawberry genome level and classified into six subgroups according to their sequence characteristics and phylogenetic relationship. Conserved motif and gene structure analysis supported the evolutionary conservation of FaERFs. Syntenic analysis showed that four types of duplication events occurred during the expansion of FaERF gene family. Of these, WGD/segmental duplication played a major role. Transcriptomic data of FaERF genes during fruit ripening and in response to abscisic acid screened one activator (FaERF316) and one repressor (FaERF118) that were involved in fruit ripening. Transcriptional regulation analysis showed some transcription factors related to ripening such as ABI4, TCP15, and GLK1 could bind to FaERF316 or FaERF118 promoters, while protein–protein interaction analysis displayed some proteins associated with plant growth and development could interact with FaERF118 or FaERF316. These results suggested that FaERF118 and FaERF316 were potential genes to regulate strawberry ripening. In summary, the present study provides the comprehensive and systematic information on FaERF family evolution and gains insights into FaERF’s potential regulatory mechanism in strawberry ripening. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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24 pages, 5763 KiB  
Article
Homokaryotic High-Quality Genome Assembly of Medicinal Fungi Wolfiporia hoelen Reveals Auto-Regulation and High-Temperature Adaption of Probable Two-Speed Genome
by Shoujian Li, Guoliang Meng and Caihong Dong
Int. J. Mol. Sci. 2022, 23(18), 10484; https://doi.org/10.3390/ijms231810484 - 10 Sep 2022
Viewed by 1625
Abstract
Sclerotia of Wolfiporia hoelen are one of the most important traditional Chinese medicines and are commonly used in China, Japan, Korea, and other Asian countries. In the present study, we presented the first high-quality homokaryotic genome of W. hoelen with 14 chromosomes which [...] Read more.
Sclerotia of Wolfiporia hoelen are one of the most important traditional Chinese medicines and are commonly used in China, Japan, Korea, and other Asian countries. In the present study, we presented the first high-quality homokaryotic genome of W. hoelen with 14 chromosomes which was evaluated with assembly index, telomere position detection, and whole-genome collinearity. A 64.44 Mb genome was assembled with a Contig N50 length of 3.76 Mb. The imbalanced distribution of transposons and chromosome characters revealed the probable two-speed genome of W. hoelen. High consistency between methylation and transposon conserved the genome stability. The expansion of the gene family about signal transduction and nutritional transport has intimate relationships with sclerotial formation. Up-regulation of expression for distinctive decomposition enzymes, ROS clearance genes, biosynthesis of unsaturated fatty acids, and change of the cell wall components maintained high-speed growth of mycelia that may be the high-temperature adaption strategy of W. hoelen. Further, the analysis of mating-control genes demonstrated that HD3 probably had no function on mating recognition, with the HD protein in a distant genetic with known species. Overall, the high-quality genome of W. hoelen provided crucial information for genome structure and stability, high-temperature adaption, and sexual and asexual process. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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19 pages, 8717 KiB  
Article
Genome-Wide Analysis of the RNase T2 Family and Identification of Interacting Proteins of Four ClS-RNase Genes in ‘XiangShui’ Lemon
by Yu-Ze Li, Jia-Wei Zhu, Wei Lin, Mo-Ying Lan, Cong Luo, Li-Ming Xia, Yi-Li Zhang, Rong-Zhen Liang, Wang-Li Hu, Gui-Xiang Huang and Xin-Hua He
Int. J. Mol. Sci. 2022, 23(18), 10431; https://doi.org/10.3390/ijms231810431 - 09 Sep 2022
Cited by 3 | Viewed by 2149
Abstract
S-RNase plays vital roles in the process of self-incompatibility (SI) in Rutaceae plants. Data have shown that the rejection phenomenon during self-pollination is due to the degradation of pollen tube RNA by S-RNase. The cytoskeleton microfilaments of pollen tubes are destroyed, and other [...] Read more.
S-RNase plays vital roles in the process of self-incompatibility (SI) in Rutaceae plants. Data have shown that the rejection phenomenon during self-pollination is due to the degradation of pollen tube RNA by S-RNase. The cytoskeleton microfilaments of pollen tubes are destroyed, and other components cannot extend downwards from the stigma and, ultimately, cannot reach the ovary to complete fertilisation. In this study, four S-RNase gene sequences were identified from the ‘XiangShui’ lemon genome and ubiquitome. Sequence analysis revealed that the conserved RNase T2 domains within S-RNases in ‘XiangShui’ lemon are the same as those within other species. Expression pattern analysis revealed that S3-RNase and S4-RNase are specifically expressed in the pistils, and spatiotemporal expression analysis showed that the S3-RNase expression levels in the stigmas, styles and ovaries were significantly higher after self-pollination than after cross-pollination. Subcellular localisation analysis showed that the S1-RNase, S2-RNase, S3-RNase and S4-RNase were found to be expressed in the nucleus according to laser confocal microscopy. In addition, yeast two-hybrid (Y2H) assays showed that S3-RNase interacted with F-box, Bifunctional fucokinase/fucose pyrophosphorylase (FKGP), aspartic proteinase A1, RRP46, pectinesterase/pectinesterase inhibitor 51 (PME51), phospholipid:diacylglycerol acyltransferase 1 (PDAT1), gibberellin receptor GID1B, GDT1-like protein 4, putative invertase inhibitor, tRNA ligase, PAP15, PAE8, TIM14-2, PGIP1 and p24beta2. Moreover, S3-RNase interacted with TOPP4. Therefore, S3-RNase may play an important role in the SI of ‘XiangShui’ lemon. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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16 pages, 3677 KiB  
Article
PbXND1 Results in a Xylem-Deficient Dwarf Phenotype through Interaction with PbTCP4 in Pear (Pyrus bretschneideri Rehd.)
by Yuxiong Xiao, Guangya Sha, Di Wang, Rui Gao, Bingqing Qie, Liu Cong, Rui Zhai, Chengquan Yang, Zhigang Wang and Lingfei Xu
Int. J. Mol. Sci. 2022, 23(15), 8699; https://doi.org/10.3390/ijms23158699 - 04 Aug 2022
Cited by 2 | Viewed by 1627
Abstract
Dwarfing is an important agronomic characteristic in fruit breeding. However, due to the lack of dwarf cultivars and dwarf stocks, the dwarfing mechanism is poorly understood in pears. In this research, we discovered that the dwarf hybrid seedlings of pear (Pyrus bretschneideri [...] Read more.
Dwarfing is an important agronomic characteristic in fruit breeding. However, due to the lack of dwarf cultivars and dwarf stocks, the dwarfing mechanism is poorly understood in pears. In this research, we discovered that the dwarf hybrid seedlings of pear (Pyrus bretschneideri Rehd.), ‘Red Zaosu,’ exhibited a xylem-deficient dwarf phenotype. The expression level of PbXND1, a suppressor of xylem development, was markedly enhanced in dwarf hybrid seedlings and its overexpression in pear results in a xylem-deficient dwarf phenotype. To further dissect the mechanism of PbXND1, PbTCP4 was isolated as a PbXND1 interaction protein through the pear yeast library. Root transformation experiments showed that PbTCP4 promotes root xylem development. Dual-luciferase assays showed that PbXND1 interactions with PbTCP4 suppressed the function of PbTCP4. PbXND1 expression resulted in a small amount of PbTCP4 sequestration in the cytoplasm and thereby prevented it from activating the gene expression, as assessed by bimolecular fluorescence complementation and co-location analyses. Additionally, PbXND1 affected the DNA-binding ability of PbTCP4, as determined by utilizing an electrophoretic mobility shift assay. These results suggest that PbXND1 regulates the function of PbTCP4 principally by affecting the DNA-binding ability of PbTCP4, whereas the cytoplasmic sequestration of PbTCP4 is only a minor factor. Taken together, this study provides new theoretical support for the extreme dwarfism associated with the absence of xylem caused by PbXND1, and it has significant reference value for the breeding of dwarf varieties and dwarf rootstocks of the pear. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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16 pages, 8063 KiB  
Article
Newly Discovered Alleles of the Tomato Antiflorigen Gene SELF PRUNING Provide a Range of Plant Compactness and Yield
by Min-Sung Kang, Yong Jun Kim, Jung Heo, Sujeevan Rajendran, Xingang Wang, Jong Hyang Bae, Zachary Lippman and Soon Ju Park
Int. J. Mol. Sci. 2022, 23(13), 7149; https://doi.org/10.3390/ijms23137149 - 28 Jun 2022
Cited by 4 | Viewed by 2571
Abstract
In tomato cultivation, a rare natural mutation in the flowering repressor antiflorigen gene SELF-PRUNING (sp-classic) induces precocious shoot termination and is the foundation in determinate tomato breeding for open field production. Heterozygous single flower truss (sft) mutants in the [...] Read more.
In tomato cultivation, a rare natural mutation in the flowering repressor antiflorigen gene SELF-PRUNING (sp-classic) induces precocious shoot termination and is the foundation in determinate tomato breeding for open field production. Heterozygous single flower truss (sft) mutants in the florigen SFT gene in the background of sp-classic provide a heterosis-like effect by delaying shoot termination, suggesting the subtle suppression of determinacy by genetic modification of the florigen–antiflorigen balance could improve yield. Here, we isolated three new sp alleles from the tomato germplasm that show modified determinate growth compared to sp-classic, including one allele that mimics the effect of sft heterozygosity. Two deletion alleles eliminated functional transcripts and showed similar shoot termination, determinate growth, and yields as sp-classic. In contrast, amino acid substitution allele sp-5732 showed semi-determinate growth with more leaves and sympodial shoots on all shoots. This translated to greater yield compared to the other stronger alleles by up to 42%. Transcriptome profiling of axillary (sympodial) shoot meristems (SYM) from sp-classic and wild type plants revealed six mis-regulated genes related to the floral transition, which were used as biomarkers to show that the maturation of SYMs in the weaker sp-5732 genotype is delayed compared to sp-classic, consistent with delayed shoot termination and semi-determinate growth. Assessing sp allele frequencies from over 500 accessions indicated that one of the strong sp alleles (sp-2798) arose in early breeding cultivars but was not selected. The newly discovered sp alleles are potentially valuable resources to quantitatively manipulate shoot growth and yield in determinate breeding programs, with sp-5732 providing an opportunity to develop semi-determinate field varieties with higher yields. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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15 pages, 5872 KiB  
Article
The Upregulated Expression of the Citrus RIN4 Gene in HLB Diseased Citrus Aids Candidatus Liberibacter Asiaticus Infection
by Chunzhen Cheng, Yun Zhong, Bin Wang, Yongyan Zhang, Huan Wu, Nonghui Jiang, Bo Wu, Yuanda Lv and Bo Jiang
Int. J. Mol. Sci. 2022, 23(13), 6971; https://doi.org/10.3390/ijms23136971 - 23 Jun 2022
Cited by 2 | Viewed by 1643
Abstract
The citrus industry has been threatened by Huanglongbing (HLB) for over a century. Here, an HLB-induced Arabidopsis RPM1-interacting protein 4 (RIN4) homologous gene was cloned from Citrus clementina, and its characteristics and function were analyzed to determine its role during [...] Read more.
The citrus industry has been threatened by Huanglongbing (HLB) for over a century. Here, an HLB-induced Arabidopsis RPM1-interacting protein 4 (RIN4) homologous gene was cloned from Citrus clementina, and its characteristics and function were analyzed to determine its role during citrus–Candidatus Liberibacter asiaticus (CLas) interactions. Quantitative real-time PCR showed that RIN4 was expressed in roots, stems, leaves and flowers, with the greatest expression level in leaves. Its expression was suppressed by gibberellic acid, indole-3-acetic acid, salicylic acid and jasmonic acid treatments, but was induced by abscisic acid and salt treatments, as well as wounding. The transient expression of a RIN4-GFP showed that RIN4 was localized in the cell membrane. RIN4-overexpressing transgenic C. maxima cv. ‘Shatianyou’ plants were obtained, and some transgenic plants showed greater sensitivity to CLas infection and earlier HLB symptoms appearance than non-transgenic controls. Results obtained in this study indicated that the upregulated expression of RIN4 in HLB diseased citrus may aid CLas infection. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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19 pages, 7350 KiB  
Article
Time-Course Transcriptomic Profiling of Floral Induction in Cultivated Strawberry
by Jiahui Liang, Jing Zheng, Ze Wu and Hongqing Wang
Int. J. Mol. Sci. 2022, 23(11), 6126; https://doi.org/10.3390/ijms23116126 - 30 May 2022
Cited by 4 | Viewed by 2012
Abstract
The initiation and quality of flowering directly affect the time to market and economic benefit of cultivated strawberries, but the underlying mechanisms of these processes are largely unknown. To investigate the gene activity during the key period of floral induction in strawberries, time-course [...] Read more.
The initiation and quality of flowering directly affect the time to market and economic benefit of cultivated strawberries, but the underlying mechanisms of these processes are largely unknown. To investigate the gene activity during the key period of floral induction in strawberries, time-course transcriptome analysis was performed on the shoot apex of the strawberry cultivar ‘Benihoppe.’ A total of 7177 differentially expressed genes (DEGs) were identified through pairwise comparisons. These DEGs were grouped into four clusters with dynamic expression patterns. By analyzing the key genes in the potential flowering pathways and the development of the leaf and flower, at least 73 DEGs that may be involved in the regulatory network of floral induction in strawberries were identified, some of which belong to the NAC, MYB, MADS, and SEB families. A variety of eight hormone signaling pathway genes that might play important roles in floral induction were analyzed. In particular, the gene encoding DELLA, a key inhibitor of the gibberellin signaling pathway, was found to be significantly differentially expressed during the floral induction. Furthermore, the differential expression of some important candidate genes, such as TFL1, SOC1, and GAI-like, was further verified by qRT-PCR. Therefore, we used this time-course transcriptome data for a preliminary exploration of the regulatory network of floral induction and to provide potential candidate genes for future studies of flowering in strawberries. Full article
(This article belongs to the Special Issue Advances in Research for Fruit Crop Breeding and Genetics)
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