Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.3
5.5
Journals
Biomolecules
Special Issues
Molecular-Genetic Basis of Plant Breeding 2.0
share announcement

Molecular-Genetic Basis of Plant Breeding 2.0

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

Deadline for manuscript submissions: closed (20 October 2023) | Viewed by 10247

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,

Following a very successful first run, we are pleased to announce the launch of the second edition of a Special Issue on the Molecular-Genetic Bases of Plant Breeding.

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, reviews and mini-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

Published Papers (7 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

14 pages, 2255 KiB  
Article
Conjunctive Analysis of BSA-Seq and SSR Markers Unveil the Candidate Genes for Resistance to Rice False Smut
by Rongtao Fu, Liyu Zhao, Cheng Chen, Jian Wang and Daihua Lu
Biomolecules 2024, 14(1), 79; https://doi.org/10.3390/biom14010079 - 8 Jan 2024
Viewed by 1064
Abstract
Rice false smut (RFS) caused by the fungus Ustilaginoidea virens (Cook) leads to serious yield losses in rice. Identification of the gene or quantitative trait loci (QTLs) is crucial to resistance breeding and mitigation of RFS damage. In this study, we crossed a [...] Read more.
Rice false smut (RFS) caused by the fungus Ustilaginoidea virens (Cook) leads to serious yield losses in rice. Identification of the gene or quantitative trait loci (QTLs) is crucial to resistance breeding and mitigation of RFS damage. In this study, we crossed a resistant variety, IR77298-14-1-2::IRGC117374-1, with a susceptible indica cultivar, 9311, and evaluated recombinant inbred lines in a greenhouse. The genetic analysis showed that the RFS resistance of IR77298-14-1-2::IRGC117374-1 was controlled by multiple recessive loci. We identified a novel QTL, qRFS12.01, for RFS resistance in IR77298-14-1-2::IRGC117374-1 by combining bulked segregant analysis with whole genome resequencing (BSA-seq) and simple sequence repeat (SSR) marker mapping approaches. The phenotypic effect of qRFS12.01 on RFS resistance reached 28.74%, suggesting that SSR markers linked to qRFS12.01 are valuable for marker-assisted breeding of RFS resistance in rice. The prediction of putative candidate genes within qRFS12.01 revealed five disease resistance proteins containing NB-ARC domains. In conclusion, our findings provide a new rice chromosome region carrying genes/QTLs for resistance to RFS. Full article
(This article belongs to the Special Issue Molecular-Genetic Basis of Plant Breeding 2.0)
►▼ Show Figures

Figure 1

20 pages, 7721 KiB  
Article
Genome-Wide Identification and Characterization of Long Non-Coding RNAs Associated with Floral Scent Formation in Jasmine (Jasminum sambac)
by Zhaogeng Lu, Xinwen Wang, Xinyi Lin, Salma Mostafa, Hongyan Bao, Shixiong Ren, Jiawen Cui and Biao Jin
Biomolecules 2024, 14(1), 45; https://doi.org/10.3390/biom14010045 - 28 Dec 2023
Viewed by 990
Abstract
Long non-coding RNAs (lncRNAs) have emerged as curial regulators of diverse biological processes in plants. Jasmine (Jasminum sambac) is a world-renowned ornamental plant for its attractive and exceptional flower fragrance. However, to date, no systematic screening of lncRNAs and their regulatory [...] Read more.
Long non-coding RNAs (lncRNAs) have emerged as curial regulators of diverse biological processes in plants. Jasmine (Jasminum sambac) is a world-renowned ornamental plant for its attractive and exceptional flower fragrance. However, to date, no systematic screening of lncRNAs and their regulatory roles in the production of the floral fragrance of jasmine flowers has been reported. In this study, we identified a total of 31,079 novel lncRNAs based on an analysis of strand-specific RNA-Seq data from J. sambac flowers at different stages. The lncRNAs identified in jasmine flowers exhibited distinct characteristics compared with protein-coding genes (PCGs), including lower expression levels, shorter transcript lengths, and fewer exons. Certain jasmine lncRNAs possess detectable sequence conservation with other species. Expression analysis identified 2752 differentially expressed lncRNAs (DE_lncRNAs) and 8002 DE_PCGs in flowers at the full-blooming stage. DE_lncRNAs could potentially cis- and trans-regulate PCGs, among which DE_lincRNAs and their targets showed significant opposite expression patterns. The flowers at the full-blooming stage are specifically enriched with abundant phenylpropanoids and terpenoids potentially contributed by DE_lncRNA cis-regulated PCGs. Notably, we found that many cis-regulated DE_lncRNAs may be involved in terpenoid and phenylpropanoid/benzenoid biosynthesis pathways, which potentially contribute to the production of jasmine floral scents. Our study reports numerous jasmine lncRNAs and identifies floral-scent-biosynthesis-related lncRNAs, which highlights their potential functions in regulating the floral scent formation of jasmine and lays the foundations for future molecular breeding. Full article
(This article belongs to the Special Issue Molecular-Genetic Basis of Plant Breeding 2.0)
►▼ Show Figures

Figure 1

18 pages, 8111 KiB  
Article
WRKY Transcription Factors in Jasminum sambac: An Insight into the Regulation of Aroma Synthesis
by Zhaogeng Lu, Xinwen Wang, Salma Mostafa, Iqra Noor, Xinyi Lin, Shixiong Ren, Jiawen Cui and Biao Jin
Biomolecules 2023, 13(12), 1679; https://doi.org/10.3390/biom13121679 - 21 Nov 2023
Cited by 2 | Viewed by 1008
Abstract
WRKY transcription factors are one of the largest families of transcription regulators that play essential roles in regulating the synthesis of secondary metabolites in plants. Jasmine (Jasminum sambac), renowned for its aromatic nature and fragrant blossoms, possesses a significant abundance of [...] Read more.
WRKY transcription factors are one of the largest families of transcription regulators that play essential roles in regulating the synthesis of secondary metabolites in plants. Jasmine (Jasminum sambac), renowned for its aromatic nature and fragrant blossoms, possesses a significant abundance of volatile terpene compounds. However, the role of the WRKY family in terpene synthesis in jasmine remains undetermined. In this study, 72 WRKY family genes of J. sambac were identified with their conserved WRKY domains and were categorized into three main groups based on their structural and phylogenetic characteristics. The extensive segmental duplications contributed to the expansion of the WRKY gene family. Expression profiles derived from the transcriptome data and qRT-PCR analysis showed that the majority of JsWRKY genes were significantly upregulated in fully bloomed flowers compared to buds. Furthermore, multiple correlation analyses revealed that the expression patterns of JsWRKYs (JsWRKY27/33/45/51/55/57) were correlated with both distinct terpene compounds (monoterpenes and sesquiterpenes). Notably, the majority of jasmine terpene synthase (JsTPS) genes related to terpene synthesis and containing W-box elements exhibited a significant correlation with JsWRKYs, particularly with JsWRKY51, displaying a strong positive correlation. A subcellular localization analysis showed that JsWRKY51 was localized in the nucleus. Moreover, transgenic tobacco leaves and jasmine calli experiments demonstrated that overexpression of JsWRKY51 was a key factor in enhancing the accumulation of β-ocimene, which is an important aromatic terpene component. Collectively, our findings suggest the roles of JsWRKY51 and other JsWRKYs in regulating the synthesis of aromatic compounds in J. sambac, providing a foundation for the potential utilization of JsWRKYs to facilitate the breeding of fragrant plant varieties with an improved aroma. Full article
(This article belongs to the Special Issue Molecular-Genetic Basis of Plant Breeding 2.0)
►▼ Show Figures

Figure 1

19 pages, 3511 KiB  
Article
Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan
by Raushan Yerzhebayeva, Svetlana Didorenko, Aigul Amangeldiyeva, Aliya Daniyarova, Shynar Mazkirat, Alyona Zinchenko and Yuri Shavrukov
Biomolecules 2023, 13(7), 1146; https://doi.org/10.3390/biom13071146 - 18 Jul 2023
Viewed by 1693
Abstract
The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, [...] Read more.
The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, the production and distribution of new varieties of soybeans adapted to widespread agricultural regions in northern Kazakhstan is in strong demand. Eleven soybean hybrid populations were obtained from crosses between 17 parents with four maturity groups, MG 000, 00, 0, and I. Marker-assisted selection (MAS) was assessed for suitable SSR markers and successfully applied for genes E1, E3, E4, and E7, targeting homozygous genotypes with recessive alleles. The identified and selected genotypes were propagated and tested in the conditions of 53° N latitude in the Kostanay region of northern Kazakhstan. Finally, 20 early maturing F4 breeding lines were identified and developed with genotypes e1 e3 E4 e7, e1 E3 E4 e7, and e1 E3 e4 e7, all completing their growth period within 92–102 days. These breeding lines were developed by MAS and should provide very prospective superior varieties of soybean for northern Kazakhstan through a strategy that may be very helpful to other countries with high latitudes. Full article
(This article belongs to the Special Issue Molecular-Genetic Basis of Plant Breeding 2.0)
►▼ Show Figures

Figure 1

16 pages, 1303 KiB  
Article
Genetic Dissection of Spike Productivity Traits in the Siberian Collection of Spring Barley
by Irina V. Rozanova, Yuriy N. Grigoriev, Vadim M. Efimov, Alexander V. Igoshin and Elena K. Khlestkina
Biomolecules 2023, 13(6), 909; https://doi.org/10.3390/biom13060909 - 30 May 2023
Viewed by 1090
Abstract
Barley (Hordeum vulgare L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity [...] Read more.
Barley (Hordeum vulgare L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity traits in Siberian spring barley and to develop diagnostic DNA markers for marker-assisted breeding programs. For this purpose we conducted a genome-wide association study using a panel of 94 barley varieties. In total, 64 SNPs significantly associated with productivity traits were revealed. Twenty-three SNP markers were validated by genotyping in an independent sample set using competitive allele-specific PCR (KASP). Finally, fourteen markers associated with spike productivity traits on chromosomes 2H, 4H and 5H can be suggested for use in breeding programs. Full article
(This article belongs to the Special Issue Molecular-Genetic Basis of Plant Breeding 2.0)
►▼ Show Figures

Figure 1

19 pages, 6780 KiB  
Article
Molecular Breeding for Incorporation of Submergence Tolerance and Durable Bacterial Blight Resistance into the Popular Rice Variety ‘Ranidhan’
by Shibani Mohapatra, Saumya Ranjan Barik, Prasanta K. Dash, Devidutta Lenka, Kartika Chandra Pradhan, Reshmi Raj K. R, Shakti Prakash Mohanty, Mihir Ranjan Mohanty, Ambika Sahoo, Binod Kumar Jena, Alok Kumar Panda, Debabrata Panigrahi, Sushanta Kumar Dash, Jitendriya Meher, Chitta Ranjan Sahoo, Arup Kumar Mukherjee, Lipi Das, Lambodar Behera and Sharat Kumar Pradhan
Biomolecules 2023, 13(2), 198; https://doi.org/10.3390/biom13020198 - 18 Jan 2023
Cited by 5 | Viewed by 2053
Abstract
Ranidhan is a popular late-maturing rice variety of Odisha state, India. The farmers of the state suffer heavy loss in years with flash floods as the variety is sensitive to submergence. Bacterial blight (BB) disease is a major yield-limiting factor, and the variety [...] Read more.
Ranidhan is a popular late-maturing rice variety of Odisha state, India. The farmers of the state suffer heavy loss in years with flash floods as the variety is sensitive to submergence. Bacterial blight (BB) disease is a major yield-limiting factor, and the variety is susceptible to the disease. BB resistance genes Xa21, xa13, and xa5, along with the Sub1 QTL, for submergence stress tolerance were transferred into the variety using marker-assisted backcross breeding approach. Foreground selection using direct and closely linked markers detected the progenies carrying all four target genes in the BC1F1, BC2F1, and BC3F1 generations, and the positive progenies carrying these genes with maximum similarity to the recipient parent, Ranidhan, were backcrossed into each segregating generation. Foreground selection in the BC1F1 generation progenies detected all target genes in 11 progenies. The progeny carrying all target genes and similar to the recipient parent in terms of phenotype was backcrossed, and a total of 321 BC2F1 seeds were produced. Ten progenies carried all target genes/QTL in the BC2F1 generation. Screening of the BC3F1 progenies using markers detected 12 plants carrying the target genes. A total of 1270 BC3F2 seeds were obtained from the best BC3F1 progeny. Foreground selection in the BC3F2 progenies detected four plants carrying the target genes in the homozygous condition. The bioassay of the pyramided lines conferred very high levels of resistance to the predominant isolates of bacterial blight pathogen. These BB pyramided lines were submergence-tolerant and similar to Ranidhan in 13 agro-morphologic and grain quality traits; hence, they are likely to be adopted by farmers. Full article
(This article belongs to the Special Issue Molecular-Genetic Basis of Plant Breeding 2.0)
►▼ Show Figures

Figure 1

24 pages, 4895 KiB  
Article
Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice (Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1
by Neng Zhao, Ruizhi Yuan, Babar Usman, Jiaming Qin, Jinlian Yang, Liyun Peng, Enerand Mackon, Fang Liu, Baoxiang Qin and Rongbai Li
Biomolecules 2022, 12(12), 1850; https://doi.org/10.3390/biom12121850 - 11 Dec 2022
Cited by 1 | Viewed by 1485
Abstract
Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient’s genetic background. CSSLs are [...] Read more.
Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient’s genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12,565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide. Full article
(This article belongs to the Special Issue Molecular-Genetic Basis of Plant Breeding 2.0)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-7
Back to TopTop