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Molecular-Genetic Bases of Plant Breeding
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Molecular-Genetic Bases of Plant Breeding

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 33101

Special Issue Editors

Prof. Dr. Elena Khlestkina

E-Mail Website
Guest Editor
N. I. Vavilov All-Russian Institute of Plant Genetic Resources, Bol'shaya Morskaya Str., 42, St. Petersburg, Russia
Interests: barley; wheat; potato; genome editing; molecular markers; marker-assisted selection; molecular genetics; transcriptomics; flavonoids; anthocyanins
Special Issues, Collections and Topics in MDPI journals
Dr. Yuri Shavrukov

E-Mail Website
Guest Editor
Adjunct Professor, College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA 5042, Australia
Interests: plant biology; genetics; molecular markers; gene study and genetic analysis; genetic transformation and gene editing; tolerance to abiotic stresses; application of molecular markers; molecular plant breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Traditional plant breeding can be improved significantly through the application of molecular and genetic approaches. Starting from the basis of molecular markers and marker-assisted selection, these methods are becoming increasingly routine in crop breeding. Whether it be plant genotyping focused on individual genes in an experiment or on thousands of genes simultaneously in microarray, these methods are integral to the progression of modern plant-breeding programs. Crosses and segregations can be used to generate various types of doubled haploid and recombinant inbred lines, but genome-wide association mapping presents a powerful tool for comparative molecular-genetic analysis without hybridization. The expression of the identified genes can also be studied in individual analyses or through RNAseq methods, and these tools are very informative for plant breeding. An important component of modern plant breeding deals with proteomics and other biomolecules. Analyses of individual polypeptides and screens comparing the different profiles of a wide variety of proteins improve our knowledge of the molecular-genetic basis of plant biology as applied to crop breeding.

The aim of the Special Issue is to show the current status of our understanding and research on the molecular-genetic basis of plant breeding. The scope covers a wide and diverse breadth of modern technologies, scientific approaches and research to better understand all aspects of the modern plant breeding of crops, including both native and commercially important plant species. We encourage the submission of completed studies or research into any aspect of molecular and genetic analyses in plants that is applicable to plant breeding for inclusion in this Special Issue. We especially welcome multidisciplinary scientific papers and reviews that promote a clear and wider vision of the topic.

Potential topics include, but are not limited to, the following: plant genetics and applications in plant breeding, marker-assisted plant genetic resources studies, plant development and stress responses, gene expression and regulation in plants, genetics and molecular analyses, Mendelian genetics and epigenetics in plant breeding, molecular markers for breeding programs, molecular genetics, gene structure and function in plants, new target genes for Cas endonuclease-mediated editing, marker-assisted selection in plant breeding, the creation of mutant breeding lines using genome-editing tools, and plant population genetics and bioinformatics for breeding programs.

Prof. Dr. Elena Khlestkina
Dr. Yuri Shavrukov
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Application of molecular genetics in plant breeding
  • Candidate gene cloning
  • Gene analysis in plants
  • Gene editing in crop plants
  • Genetic mapping in crop plants
  • Genetic resources studies in plants
  • Genomic selection
  • GWAS in crop plants
  • Marker-assisted selection
  • Molecular markers
  • Molecular plant breeding
  • Next-generation breeding
  • Plant genetics

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Editorial

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2 pages, 168 KiB  
Editorial
Molecular-Genetic Basis of Plant Breeding
by Elena Khlestkina and Yuri Shavrukov
Biomolecules 2022, 12(10), 1392; https://doi.org/10.3390/biom12101392 - 29 Sep 2022
Viewed by 1088
Abstract
Traditional plant breeding can be improved significantly through the application of molecular and genetic approaches [...] Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)

Research

Jump to: Editorial

16 pages, 3196 KiB  
Article
Comparative Transcriptome Analysis Reveals Hormone Signal Transduction and Sucrose Metabolism Related Genes Involved in the Regulation of Anther Dehiscence in Photo-Thermo-Sensitive Genic Male Sterile Wheat
by Tianbao Zhang, Shaohua Yuan, Zihan Liu, Liqing Luo, Haoyu Guo, Yanmei Li, Jianfang Bai, Changping Zhao and Liping Zhang
Biomolecules 2022, 12(8), 1149; https://doi.org/10.3390/biom12081149 - 20 Aug 2022
Cited by 2 | Viewed by 1795
Abstract
Anther dehiscence is an important process to release pollen and then is a critical event in pollination. In the wheat photo-thermo-sensitive genic male sterility (PTGMS) line, pollen cannot release from anther since the anther cannot dehisce during anther dehiscence stage in a sterile [...] Read more.
Anther dehiscence is an important process to release pollen and then is a critical event in pollination. In the wheat photo-thermo-sensitive genic male sterility (PTGMS) line, pollen cannot release from anther since the anther cannot dehisce during anther dehiscence stage in a sterile condition. In this study, we carried out RNA-sequencing to analyze the transcriptome of one wheat PTGMS line BS366 during anther dehiscence under fertile and sterile conditions to explore the mechanism. We identified 6306 differentially expressed genes (DEGs). Weighted gene co-expression network analysis (WGCNA) and KEGG analysis showed that DEGs were mainly related to “hormone signal transduction pathway” and “starch and sucrose metabolism”. We identified 35 and 23 DEGs related hormone signal transduction and sucrose metabolism, respectively. Compared with conventional wheat Jing411, there were some changes in the contents of hormones, including JA, IAA, BR, ABA and GA3, and sucrose, during three anther dehiscence stages in the sterile condition in BS366. We performed qRT-PCR to verify the expression levels of some critical DEGs of the hormone signaling pathway and the starch and sucrose metabolism pathway. The results showed disparate expression patterns of the critical DEGs of the hormone signaling pathway and the starch and sucrose metabolism pathway in different conditions, suggesting these genes may be involved in the regulation of the anther dehiscence in BS366. Finally, we conducted a hypothesis model to reveal the regulation pathway of hormones and sucrose on anther dehiscence. The information provided new clues to the molecular mechanisms of anther dehiscence in wheat and improved wheat hybrid breeding. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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27 pages, 6853 KiB  
Article
Combined Analysis of BSA-Seq Based Mapping, RNA-Seq, and Metabolomic Unraveled Candidate Genes Associated with Panicle Grain Number in Rice (Oryza sativa L.)
by Yafei Ma, Enerand Mackon, Guibeline Charlie Jeazet Dongho Epse Mackon, Yitong Zhao, Qiufeng Li, Xianggui Dai, Yuhang Yao, Xiuzhong Xia, Baoxuan Nong and Piqing Liu
Biomolecules 2022, 12(7), 918; https://doi.org/10.3390/biom12070918 - 29 Jun 2022
Cited by 8 | Viewed by 2202
Abstract
Rice grain yield is a complex and highly variable quantitative trait consisting of several key components, including the grain weight, the effective panicles per unit area, and the grain number per panicle (GNPP). The GNPP is a significant contributor to grain yield controlled [...] Read more.
Rice grain yield is a complex and highly variable quantitative trait consisting of several key components, including the grain weight, the effective panicles per unit area, and the grain number per panicle (GNPP). The GNPP is a significant contributor to grain yield controlled by multiple genes (QTL) and is crucial for improvement. Attempts have been made to find genes for this trait, which has always been a challenging and arduous task through conventional methods. We combined a BSA analysis, RNA profiling, and a metabolome analysis in the present study to identify new candidate genes involved in the GNPP. The F2 population from crossing R4233 (high GNPP) and Ce679 (low GNPP) revealed a frequency distribution fitting two segregated genes. Three pools, including low, middle, and high GNPP, were constructed and a BSA analysis revealed six candidate regions spanning 5.38 Mb, containing 739 annotated genes. Further, a conjunctive analysis of BSA-Seq and RNA-Seq showed 31 differentially expressed genes (DEGs) in the candidate intervals. Subsequently, a metabolome analysis showed 1024 metabolites, with 71 significantly enriched, including 44 up and 27 downregulated in Ce679 vs. R4233. A KEGG enrichment analysis of these 31 DEGs and 71 differentially enriched metabolites (DEMs) showed two genes, Os12g0102100 and Os01g0580500, significantly enriched in the metabolic pathways’ biosynthesis of secondary metabolites, cysteine and methionine metabolism, and fatty acid biosynthesis. Os12g0102100, which encodes for the alcohol dehydrogenase superfamily and a zinc-containing protein, is a novel gene whose contribution to the GNPP is not yet elucidated. This gene coding for mitochondrial trans-2-enoyl-CoA reductase is involved in the biosynthesis of myristic acid, also known as tetradecanoic acid. The Os01g0580500 coding for the enzyme 1-aminoclopropane-1-carboxylate oxidase (OsACO7) is responsible for the final step of the ethylene biosynthesis pathway through the conversion of 1-aminocyclopropane-1-carboxylic acid (ACC) into ethylene. Unlike Os12g0102100, this gene was significantly upregulated in R4233, downregulated in Ce679, and significantly enriched in two of the three metabolite pathways. This result pointed out that these two genes are responsible for the difference in the GNPP in the two cultivars, which has never been identified. Further validation studies may disclose the physiological mechanisms through which they regulate the GNPP in rice. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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14 pages, 1659 KiB  
Article
Flavonoid Biosynthesis Genes in Triticum aestivum L.: Methylation Patterns in Cis-Regulatory Regions of the Duplicated CHI and F3H Genes
by Ksenia Strygina and Elena Khlestkina
Biomolecules 2022, 12(5), 689; https://doi.org/10.3390/biom12050689 - 11 May 2022
Cited by 2 | Viewed by 1903
Abstract
Flavonoids are a diverse group of secondary plant metabolites that play an important role in the regulation of plant development and protection against stressors. The biosynthesis of flavonoids occurs through the activity of several enzymes, including chalcone isomerase (CHI) and flavanone 3-hydroxylase (F3H). [...] Read more.
Flavonoids are a diverse group of secondary plant metabolites that play an important role in the regulation of plant development and protection against stressors. The biosynthesis of flavonoids occurs through the activity of several enzymes, including chalcone isomerase (CHI) and flavanone 3-hydroxylase (F3H). A functional divergence between some copies of the structural TaCHI and TaF3H genes was previously shown in the allohexaploid bread wheat Triticum aestivum L. (BBAADD genome). We hypothesized that the specific nature of TaCHI and TaF3H expression may be induced by the methylation of the promoter. It was found that the predicted position of CpG islands in the promoter regions of the analyzed genes and the actual location of methylation sites did not match. We found for the first time that differences in the methylation status could affect the expression of TaCHI copies, but not the expression of TaF3Hs. At the same time, we revealed significant differences in the structure of the promoters of only the TaF3H genes, while the TaCHI promoters were highly homologous. We assume that the promoter structure in TaF3Hs primarily affects the change in the nature of gene expression. The data obtained are important for understanding the mechanisms that regulate the synthesis of flavonoids in allopolyploid wheat and show that differences in the structure of promoters have a key effect on gene expression. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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21 pages, 7602 KiB  
Article
Grapevine DMR6-1 Is a Candidate Gene for Susceptibility to Downy Mildew
by Carlotta Pirrello, Giulia Malacarne, Marco Moretto, Luisa Lenzi, Michele Perazzolli, Tieme Zeilmaker, Guido Van den Ackerveken, Stefania Pilati, Claudio Moser and Lisa Giacomelli
Biomolecules 2022, 12(2), 182; https://doi.org/10.3390/biom12020182 - 22 Jan 2022
Cited by 11 | Viewed by 4246
Abstract
Grapevine (Vitis vinifera) is a valuable crop in Europe for both economical and cultural reasons, but highly susceptible to Downy mildew (DM). The generation of resistant vines is of critical importance for a sustainable viticulture and can be achieved either by [...] Read more.
Grapevine (Vitis vinifera) is a valuable crop in Europe for both economical and cultural reasons, but highly susceptible to Downy mildew (DM). The generation of resistant vines is of critical importance for a sustainable viticulture and can be achieved either by introgression of resistance genes in susceptible varieties or by mutation of Susceptibility (S) genes, e.g., by gene editing. This second approach offers several advantages: it maintains the genetic identity of cultivars otherwise disrupted by crossing and generally results in a broad-spectrum and durable resistance, but it is hindered by the poor knowledge about S genes in grapevines. Candidate S genes are Downy mildew Resistance 6 (DMR6) and DMR6-Like Oxygenases (DLOs), whose mutations confer resistance to DM in Arabidopsis. In this work, we show that grapevine VviDMR6-1 complements the Arabidopsis dmr6-1 resistant mutant. We studied the expression of grapevine VviDMR6 and VviDLO genes in different organs and in response to the DM causative agent Plasmopara viticola. Through an automated evaluation of causal relationships among genes, we show that VviDMR6-1, VviDMR6-2, and VviDLO1 group into different co-regulatory networks, suggesting distinct functions, and that mostly VviDMR6-1 is connected with pathogenesis-responsive genes. Therefore, VviDMR6-1 represents a good candidate to produce resistant cultivars with a gene-editing approach. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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19 pages, 23804 KiB  
Article
Differentially Expressed Genes Related to Flowering Transition between Once- and Continuous-Flowering Roses
by Xingwan Yi, Huabei Gao, Yi Yang, Shumin Yang, Le Luo, Chao Yu, Jia Wang, Tangren Cheng, Qixiang Zhang and Huitang Pan
Biomolecules 2022, 12(1), 58; https://doi.org/10.3390/biom12010058 - 31 Dec 2021
Cited by 5 | Viewed by 2429
Abstract
Roses are the most important cut flower crops and widely used woody ornamental plants in gardens throughout the world, and they are model plants for studying the continuous-flowering trait of woody plants. To analyze the molecular regulation mechanism of continuous flowering, comparative transcriptome [...] Read more.
Roses are the most important cut flower crops and widely used woody ornamental plants in gardens throughout the world, and they are model plants for studying the continuous-flowering trait of woody plants. To analyze the molecular regulation mechanism of continuous flowering, comparative transcriptome data of once- and continuous-flowering roses in our previous study were used to conduct weighted gene co-expression network analysis (WGCNA) to obtain the candidate genes related to flowering transitions. The expression patterns of candidate genes at different developmental stages between Rosa chinensis “Old Blush” (continuous-flowering cultivar) and R. “Huan Die” (once-flowering cultivar) were investigated, and the relationship of the key gene with the endogenous hormone was analyzed. The results showed that the expression trends of VIN3-LIKE 1 (VIL1), FRIGIDA- LIKE 3 (FRI3), APETALA 2- LIKE (AP2-like) and CONSTANS-LIKE 2 (CO-like 2) genes were significantly different between “Old Blush” and “Huan Die”, and the expression trends of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and CO-like 2 were consistent in the flowering transition of “Old Blush” under different environments. The changes in cytokinin and gibberellic acid (GA3) content were different in the two rose cultivars. The overall change trend of the abscisic acid and GA3 in the flowering transition of “Old Blush” under different environments was consistent. The promoter sequence of CO-like 2 contained a P-box element associated with gibberellin response, as well as binding sites for transcription factors. In a word, we found CO-like 2 associated with continuous flowering and some factors that may synergistically regulate continuous flowering. The results provided a reference for elucidating the molecular regulatory mechanisms of continuous-flowering traits in roses. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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11 pages, 2346 KiB  
Article
Allelic Variation Analysis at the Vernalization Response and Photoperiod Genes in Russian Wheat Varieties Identified Two Novel Alleles of Vrn-B3
by Alina Berezhnaya, Antonina Kiseleva, Irina Leonova and Elena Salina
Biomolecules 2021, 11(12), 1897; https://doi.org/10.3390/biom11121897 - 17 Dec 2021
Cited by 10 | Viewed by 2518
Abstract
Heading time is an important agronomic trait affecting the adaptability and productivity of common wheat. In this study, 95 common wheat varieties from Russia and the late-maturing breeding line ‘Velut’ were tested for allelic diversity of genes having the strongest effect on heading. [...] Read more.
Heading time is an important agronomic trait affecting the adaptability and productivity of common wheat. In this study, 95 common wheat varieties from Russia and the late-maturing breeding line ‘Velut’ were tested for allelic diversity of genes having the strongest effect on heading. In this research, allelic variation at the Ppd-D1, Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3 loci was tested. The Vrn-B1 and Vrn-B3 loci provided the largest contribution to genetic diversity. We found two novel allelic variants of the Vrn-B3 gene in the studied varieties. Ten varieties carried a 160 bp insertion in the promoter region, and the breeding line ‘Velut’ carried a 1617 bp insertion. These alleles were designated Vrn-B3e and Vrn-B3d, respectively. The analysis of the sequences showed the recent insertion of a retrotransposon homologous to the LTR retrotransposon (RLX_Hvul_Dacia_ RND-1) in the Vrn-B3d allele. Plants with the Vrn-B3e and the ‘Velut’ line with the Vrn-B3d allele headed later than the plants with the wild-type allele; among these plants, ‘Velut’ is the latest maturing wheat variety. Analysis of the gene expression of two groups of lines differing by the Vrn-B3 alleles (Vrn-B3d or vrn-B3) from the F2 population with ‘Velut’ as a parental line did not reveal a significant difference in the expression level between the groups. Additional research is required to study the reasons for the late maturation of the ‘Velut’ line. However, the studied wheat varieties could be used as a potential source of natural variation in genes controlling heading times. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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12 pages, 2444 KiB  
Article
Identification of miRNA-Target Gene Pairs Responsive to Fusarium Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles
by Jun Xu, Qianqian Xian, Ningyuan Zhang, Ke Wang, Xin Zhou, Yansong Li, Jingping Dong and Xuehao Chen
Biomolecules 2021, 11(11), 1620; https://doi.org/10.3390/biom11111620 - 02 Nov 2021
Cited by 6 | Viewed by 2234
Abstract
Fusarium wilt (FW) of cucumber (Cucumis sativus L.) caused by Fusarium oxysporum f. sp. cucumerinum (Foc) is a destructive soil-borne disease that severely decreases cucumber yield and quality worldwide. MicroRNAs (miRNAs) are small non-coding RNAs (sRNAs) that are important for [...] Read more.
Fusarium wilt (FW) of cucumber (Cucumis sativus L.) caused by Fusarium oxysporum f. sp. cucumerinum (Foc) is a destructive soil-borne disease that severely decreases cucumber yield and quality worldwide. MicroRNAs (miRNAs) are small non-coding RNAs (sRNAs) that are important for regulating host immunity because they affect target gene expression. However, the specific miRNAs and the miRNA/target gene crosstalk involved in cucumber resistance to FW remain unknown. In this study, we compared sRNA-seq and RNA-seq data for cucumber cultivar ‘Rijiecheng’, which is resistant to FW. The integrated analysis identified FW-responsive miRNAs and their target genes. On the basis of verified expression levels, we detected two highly expressed miRNAs with down-regulated expression in response to Foc. Moreover, an analysis of 21 target genes in cucumber inoculated with Foc indicated that JRL3 (Csa2G362470), which is targeted by miR319a, and BEE1 (Csa1G024150), DAHP1 (Csa2G369040), and PERK2 (Csa4G642480), which are targeted by miR6300, are expressed at high levels, but their expression is further up-regulated after Foc inoculation. These results imply that miR319a-JRL3, miR6300-BEE1, miR6300-DAHP1 and miR6300-PERK2 regulate cucumber defenses against FW, and provide the gene resources that may be useful for breeding programs focused on developing new cucumber varieties with enhanced resistance to FW. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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16 pages, 4678 KiB  
Article
Comparative Transcriptomic Analysis Reveals the Effects of Drought on the Biosynthesis of Methyleugenol in Asarum sieboldii Miq.
by Fawang Liu, Tahir Ali and Zhong Liu
Biomolecules 2021, 11(8), 1233; https://doi.org/10.3390/biom11081233 - 18 Aug 2021
Cited by 8 | Viewed by 2352
Abstract
Asarum sieboldii Miq., a perennial herb in the family Aristolochiaceae, is widely used to treat colds, fever, headache and toothache in China. However, little is known about the drought-tolerance characteristics of A. sieboldii. In this study, to elucidate the molecular–genetic mechanisms [...] Read more.
Asarum sieboldii Miq., a perennial herb in the family Aristolochiaceae, is widely used to treat colds, fever, headache and toothache in China. However, little is known about the drought-tolerance characteristics of A. sieboldii. In this study, to elucidate the molecular–genetic mechanisms of drought-stress tolerance of A. sieboldii, RNA-seq was conducted. In total, 53,344 unigenes were assembled, and 28,715 unigenes were annotated. A total of 6444 differential-expression unigenes (DEGs) were found, which were mainly enriched in phenylpropanoid, starch and sucrose metabolic pathways. Drought stress revealed significant up-regulation of the unigenes encoding PAL, C4H, HCT, C3H, CCR and IGS in the methyleugenol-biosynthesis pathway. Under the condition of maintaining drought for 15 days and 30 days, drought stress reduced the biosynthesis of volatile oil by 24% and 38%, respectively, while the production of key medicinal ingredients (such as methyl eugenol) was increased. These results provide valuable information about the diverse mechanisms of drought resistance in the A. sieboldii, and the changes in the expression of the genes involved in methyleugenol biosynthesis in response to drought stress. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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24 pages, 4633 KiB  
Article
Evolutionary and Characteristic Analysis of RING-DUF1117 E3 Ubiquitin Ligase Genes in Gossypium Discerning the Role of GhRDUF4D in Verticillium dahliae Resistance
by Yan-Peng Zhao, Jian-Ling Shen, Wen-Jie Li, Na Wu, Chen Chen and Yu-Xia Hou
Biomolecules 2021, 11(8), 1145; https://doi.org/10.3390/biom11081145 - 03 Aug 2021
Cited by 14 | Viewed by 2485
Abstract
Verticillium wilt, primarily induced by the soil-borne fungus Verticillium dahliae, is a serious threat to cotton fiber production. There are a large number of really interesting new gene (RING) domain-containing E3 ubiquitin ligases in Arabidopsis, of which three (At2g39720 (AtRHC2A), At3g46620 (AtRDUF1), [...] Read more.
Verticillium wilt, primarily induced by the soil-borne fungus Verticillium dahliae, is a serious threat to cotton fiber production. There are a large number of really interesting new gene (RING) domain-containing E3 ubiquitin ligases in Arabidopsis, of which three (At2g39720 (AtRHC2A), At3g46620 (AtRDUF1), and At5g59550 (AtRDUF2)) have a domain of unknown function (DUF) 1117 domain in their C-terminal regions. This study aimed to detect and characterize the RDUF members in cotton, to gain an insight into their roles in cotton’s adaptation to environmental stressors. In this study, a total of 6, 7, 14, and 14 RDUF (RING-DUF1117) genes were detected in Gossypium arboretum, G. raimondii, G. hirsutum, and G. barbadense, respectively. These RDUF genes were classified into three groups. The genes in each group were highly conserved based on gene structure and domain analysis. Gene duplication analysis revealed that segmental duplication occurred during cotton evolution. Expression analysis revealed that the GhRDUF genes were widely expressed during cotton growth and under abiotic stresses. Many cis-elements related to hormone response and environment stressors were identified in GhRDUF promoters. The predicted target miRNAs and transcription factors implied that GhRDUFs might be regulated by gra-miR482c, as well as by transcription factors, including MYB, C2H2, and Dof. The GhRDUF genes responded to cold, drought, and salt stress and were sensitive to jasmonic acid, salicylic acid, and ethylene signals. Meanwhile, GhRDUF4D expression levels were enhanced after V. dahliae infection. Subsequently, GhRDUF4D was verified by overexpression in Arabidopsis and virus-induced gene silencing treatment in upland cotton. We observed that V. dahliae resistance was significantly enhanced in transgenic Arabidopsis, and weakened in GhRDUF4D silenced plants. This study conducted a comprehensive analysis of the RDUF genes in Gossypium, hereby providing basic information for further functional studies. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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12 pages, 3699 KiB  
Article
BIG3 and BIG5 Redundantly Mediate Vesicle Trafficking in Arabidopsis
by Yiping Suo, Fenhong Hu, Haojie Zhu, Di Li, Rui Qi, Jirong Huang and Wenjuan Wu
Biomolecules 2021, 11(5), 732; https://doi.org/10.3390/biom11050732 - 14 May 2021
Cited by 5 | Viewed by 4461
Abstract
Vesicle trafficking plays an important role in delivering a diverse range of cargoes between different membranous systems in eukaryotes. It is well documented that the brefeldin A (BFA)-inhibited guanine nucleotide exchange factor (GEF), named BIG, regulates vesicle budding at the trans-Golgi network [...] Read more.
Vesicle trafficking plays an important role in delivering a diverse range of cargoes between different membranous systems in eukaryotes. It is well documented that the brefeldin A (BFA)-inhibited guanine nucleotide exchange factor (GEF), named BIG, regulates vesicle budding at the trans-Golgi network (TGN) and recycling endosomes through activating the ADP-ribosylation factor (ARFs). Among the five BIGs in Arabidopsis, BIG5 is characterized to mediate ARF-dependent trafficking at the plasma membrane or endosomes while the members from BIG1 to BIG4 (BIG1-BIG4) at the TGN in the secretory pathway. However, evidence is increasing to suggest that BIG5 can function redundantly with BIG1-BIG4 to regulate vesicular trafficking in response to various intra- and extra-cellular stimuli. In this study, our genetic analysis showed that BIG5 played an overlapping role at least with BIG3 in cell proliferation. To elucidate molecular mechanisms underlying the BIG5- and BIG3-regulated biological processes, we examined the effect of BIGs on expression patterns of the two transmembrane proteins, PINFORMED 2 (PIN2) epically localized in root epidermal cells and the regulator of G protein signaling 1 (RGS1) localized in the plasma membrane. Our data showed that the PIN2 polar distribution was slightly reduced in big3 big5 in the absence of BFA, and it was significantly reduced by the treatment of 0.1 µM BFA in big3 big5. Further analysis revealed that BFA bodies derived from the plasma membrane were only observed in wild type (WT), big3 and big5 cells, but not in the big3 big5 cells. These results indicate that BIG5 and BIG3 are functionally redundant in the endosome recycling pathway from the plasma membrane to TGN. On the other hand, the single BIG3 or BIG5 mutation had no effect on the plasma membrane expression of RGS1, whereas the double mutations in BIG3 and BIG5 led to a significant amount of RGS1 retained in the vesicle, indicating that BIG3 and BIG5 act redundantly in mediating protein trafficking. Furthermore, transmission electron microscopy assays showed that Golgi ultrastructure in big3 big5 cells was abnormal and similar to that in BFA-treated WT cells. Taken together, our data provide several new lines of evidence supporting that BIGs play a redundant role in vesicular trafficking and probably also in maintaining the Golgi structural integrity in Arabidopsis. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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22 pages, 8987 KiB  
Article
Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing
by Carlotta Pirrello, Tieme Zeilmaker, Luca Bianco, Lisa Giacomelli, Claudio Moser and Silvia Vezzulli
Biomolecules 2021, 11(2), 181; https://doi.org/10.3390/biom11020181 - 28 Jan 2021
Cited by 14 | Viewed by 3406
Abstract
Several pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and the mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer [...] Read more.
Several pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and the mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity, and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted in Arabidopsis, putative genes associated with downy mildew susceptibility have been discovered also in the grapevine genome. In this work, we deep-sequenced four putative susceptibility genes—namely VvDMR6.1, VvDMR6.2, VvDLO1, VvDLO2—in 190 genetically diverse grapevine genotypes to discover new sources of broad-spectrum and recessively inherited resistance. Identified Single Nucleotide Polymorphisms were screened in a bottleneck analysis from the genetic sequence to their impact on protein structure. Fifty-five genotypes showed at least one impacting mutation in one or more of the scouted genes. Haplotypes were inferred for each gene and two of them at the VvDMR6.2 gene were found significantly more represented in downy mildew resistant genotypes. The current results provide a resource for grapevine and plant genetics and could corroborate genomic-assisted breeding programs as well as tailored gene editing approaches for resistance to biotic stresses. Full article
(This article belongs to the Special Issue Molecular-Genetic Bases of Plant Breeding)
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