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Genetics and Multi-Omics for Crop Breeding

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 31 May 2024 | Viewed by 8423

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Prof. Dr. Ludmila Khrustaleva

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Guest Editor

1. Russian State Agrarian University-Moscow Timiryazev Agricultural Academy (RGAU-MTAA), 49, Timiryazevskaya Str., 127550 Moscow, Russia
2. All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskay 42 Str., 127550 Moscow, Russia
Interests: plant molecular cytogenetics; recombination; genomics; genome editing

Special Issue Information

Dear Colleagues,

Plant products such as bread, oil, vegetables and fruits are present in our everyday diet. Ornamental plants make our life more colorful and bring us a sense of beauty. All the abundance and diversity of plant products we have today thanks, in particular, to plant breeding. Plant breeding is an ancient human activity that has come a long way in the evolution from primitive selection, further based on genetics through molecular selection (MAS) to multi-omics approaches. The rapid progress in genome sequencing and handling very large datasets have opened boundless prospects in genome study and gene manipulations. In silico analysis allows prediction of promotor region, regulator elements and coding regions of genes in non-sequenced crops based on sequenced species. Molecular cytogenetics bridges the gap between in silico genome analysis and in vivo organization. With NGS technologies, the genomic sequences of many important crops are available, facilitating genome editing approaches to create new allelic variants in the genomes of cultivated individuals. Over the past decades we unravel how mitochondria are involved in triggering death of the male reproductive organs. Cytoplasmic mail sterility (CMS) is successfully used in plant breeding, so the study of genotype polymorphisms in the mitochondrial DNAs across commercially used sources of CMS and discover of new CMS system are of great importance for both basic and applied research.

This Special Issue welcomes high-quality research articles and reviews that advance our knowledge of plant molecular biology and demonstrate the power of multi-omics approaches in crop breeding. Topics covered by this issue include but are not limited to:

Multi-omics analysis pipelines as a breeding tool;
CMS;
Genome editing;
Molecular cytogenetics in plant breeding.

Prof. Dr. Ludmila Khrustaleva
Guest Editor

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Published Papers (7 papers)

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Research

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16 pages, 10554 KiB

Open AccessArticle

The Characterization of G-Quadruplexes in Tobacco Genome and Their Function under Abiotic Stress

by Kangkang Song, Bin Li, Haozhen Li, Rui Zhang, Xiaohua Zhang, Ruiwei Luan, Ying Liu and Long Yang

Int. J. Mol. Sci. 2024, 25(8), 4331; https://doi.org/10.3390/ijms25084331 - 14 Apr 2024

Viewed by 343

Abstract

Tobacco is an ideal model plant in scientific research. G-quadruplex is a guanine-rich DNA structure, which regulates transcription and translation. In this study, the prevalence and potential function of G-quadruplexes in tobacco were systematically analyzed. In tobacco genomes, there were 2,924,271,002 G-quadruplexes in the nuclear genome, 430,597 in the mitochondrial genome, and 155,943 in the chloroplast genome. The density of the G-quadruplex in the organelle genome was higher than that in the nuclear genome. G-quadruplexes were abundant in the transcription regulatory region of the genome, and a difference in G-quadruplex density in two DNA strands was also observed. The promoter of 60.4% genes contained at least one G-quadruplex. Compared with up-regulated differentially expressed genes (DEGs), the G-quadruplex density in down-regulated DEGs was generally higher under drought stress and salt stress. The G-quadruplex formed by simple sequence repeat (SSR) and its flanking sequence in the promoter region of the NtBBX (Nitab4.5_0002943g0010) gene might enhance the drought tolerance of tobacco. This study lays a solid foundation for further research on G-quadruplex function in tobacco and other plants. Full article

(This article belongs to the Special Issue Genetics and Multi-Omics for Crop Breeding)

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16 pages, 3558 KiB

Open AccessArticle

Identification of MATE Family and Characterization of GmMATE13 and GmMATE75 in Soybean’s Response to Aluminum Stress

by Pengxiang Gao, Rongrong Han, Hui Xu, Yunmin Wei and Yongxiong Yu

Int. J. Mol. Sci. 2024, 25(7), 3711; https://doi.org/10.3390/ijms25073711 - 26 Mar 2024

Viewed by 359

Abstract

The multidrug and toxic compound extrusion (MATE) proteins are coding by a secondary transporter gene family, and have been identified to participate in the modulation of organic acid exudation for aluminum (Al) resistance. The soybean variety Glycine max “Tamba” (TBS) exhibits high Al tolerance. The expression patterns of MATE genes in response to Al stress in TBS and their specific functions in the context of Al stress remain elusive. In this study, 124 MATE genes were identified from the soybean genome. The RNA-Seq results revealed significant upregulation of GmMATE13 and GmMATE75 in TBS upon exposure to high-dose Al³⁺ treatment and both genes demonstrated sequence homology to citrate transporters of other plants. Subcellular localization showed that both proteins were located in the cell membrane. Transgenic complementation experiments of Arabidopsis mutants, atmate, with GmMATE13 or GmMATE75 genes enhanced the Al tolerance of the plant due to citrate secretion. Taken together, this study identified GmMATE13 and GmMATE75 as citrate transporter genes in TBS, which could improve citrate secretion and enhance Al tolerance. Our findings provide genetic resources for the development of plant varieties that are resistant to Al toxicity. Full article

(This article belongs to the Special Issue Genetics and Multi-Omics for Crop Breeding)

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17 pages, 6672 KiB

Open AccessArticle

Physiological and Transcriptomic Analysis Reveals That Melatonin Alleviates Aluminum Toxicity in Alfalfa (Medicago sativa L.)

by Congge Liu, Haijing Cheng, Shuwei Wang, Dashi Yu and Yunmin Wei

Int. J. Mol. Sci. 2023, 24(24), 17221; https://doi.org/10.3390/ijms242417221 - 07 Dec 2023

Cited by 1 | Viewed by 794

Abstract

Aluminum (Al) toxicity is the most common factor limiting the growth of alfalfa in acidic soil conditions. Melatonin (MT), a significant pleiotropic molecule present in both plants and animals, has shown promise in mitigating Al toxicity in various plant species. This study aims to elucidate the underlying mechanism by which melatonin alleviates Al toxicity in alfalfa through a combined physiological and transcriptomic analysis. The results reveal that the addition of 5 μM melatonin significantly increased alfalfa root length by 48% and fresh weight by 45.4% compared to aluminum treatment alone. Moreover, the 5 μM melatonin application partially restored the enlarged and irregular cell shape induced by aluminum treatment, resulting in a relatively compact arrangement of alfalfa root cells. Moreover, MT application reduces Al accumulation in alfalfa roots and shoots by 28.6% and 27.6%, respectively. Additionally, MT plays a crucial role in scavenging Al-induced excess H₂O₂ by enhancing the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), consequently reducing malondialdehyde (MDA) levels. More interestingly, the RNA-seq results reveal that MT application significantly upregulates the expression of xyloglucan endotransglucosylase/hydrolase (XTH) and carbon metabolism-related genes, including those involved in the glycolysis process, as well as sucrose and starch metabolism, suggesting that MT application may mitigate Al toxicity by facilitating the binding of Al to the cell walls, thereby reducing intracellular Al accumulation, and improving respiration and the content of sucrose and trehalose. Taken together, our study demonstrates that MT alleviates Al toxicity in alfalfa by reducing Al accumulation and restoring redox homeostasis. These RNA-seq results suggest that the alleviation of Al toxicity by MT may occur through its influence on cell wall composition and carbon metabolism. This research advances our understanding of the mechanisms underlying MT’s effectiveness in mitigating Al toxicity, providing a clear direction for our future investigations into the underlying mechanisms by which MT alleviates Al toxicity in alfalfa. Full article

(This article belongs to the Special Issue Genetics and Multi-Omics for Crop Breeding)

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21 pages, 18929 KiB

Open AccessArticle

The Control of the Crossover Localization in Allium

by Natalia Kudryavtseva, Aleksey Ermolaev, Anton Pivovarov, Sergey Simanovsky, Sergey Odintsov and Ludmila Khrustaleva

Int. J. Mol. Sci. 2023, 24(8), 7066; https://doi.org/10.3390/ijms24087066 - 11 Apr 2023

Viewed by 1786

Abstract

Meiotic crossovers/chiasmata are not randomly distributed and strictly controlled. The mechanisms behind crossover (CO) patterning remain largely unknown. In Allium cepa, as in the vast majority of plants and animals, COs predominantly occur in the distal 2/3 of the chromosome arm, while in Allium fistulosum they are strictly localized in the proximal region. We investigated the factors that may contribute to the pattern of COs in A. cepa, A. fistulosum and their F

_{1}

diploid (2n = 2x = 8C + 8F) and F

_{1}

triploid (2n = 3x = 16F + 8C) hybrids. The genome structure of F

_{1}

hybrids was confirmed using genomic in situ hybridization (GISH). The analysis of bivalents in the pollen mother cells (PMCs) of the F

_{1}

triploid hybrid showed a significant shift in the localization of COs to the distal and interstitial regions. In F

_{1}

diploid hybrid, the COs localization was predominantly the same as that of the A. cepa parent. We found no differences in the assembly and disassembly of ASY1 and ZYP1 in PMCs between A. cepa and A. fistulosum, while F

_{1}

diploid hybrid showed a delay in chromosome pairing and a partial absence of synapsis in paired chromosomes. Immunolabeling of MLH1 (class I COs) and MUS81 (class II COs) proteins showed a significant difference in the class I/II CO ratio between A. fistulosum (50%:50%) and A. cepa (73%:27%). The MLH1:MUS81 ratio at the homeologous synapsis of F

_{1}

diploid hybrid (70%:30%) was the most similar to that of the A. cepa parent. F

_{1}

triploid hybrid at the A. fistulosum homologous synapsis showed a significant increase in MLH1:MUS81 ratio (60%:40%) compared to the A. fistulosum parent. The results suggest possible genetic control of CO localization. Other factors affecting the distribution of COs are discussed. Full article

(This article belongs to the Special Issue Genetics and Multi-Omics for Crop Breeding)

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14 pages, 966 KiB

Open AccessArticle

Two-Step Identification of N-, S-, R- and T-Cytoplasm Types in Onion Breeding Lines Using High-Resolution Melting (HRM)-Based Markers

by Ludmila Khrustaleva, Mais Nzeha, Aleksey Ermolaev, Ekaterina Nikitina and Valery Romanov

Int. J. Mol. Sci. 2023, 24(2), 1605; https://doi.org/10.3390/ijms24021605 - 13 Jan 2023

Cited by 2 | Viewed by 1546

Abstract

High-resolution melting (HRM) analysis is a powerful detection method for fast, high-throughput post-PCR analysis. A two-step HRM marker system was developed for identification of the N-, S-, R- and T-cytoplasms of onion. In the first step for the identification of N-, S- and R-cytoplasms, one forward primer was designed to the identical sequences of both cox1 and orf725 genes, and two reverse primers specific to the polymorphic sequences of cox1 and orf725 genes were used. For the second step, breeding lines with N-cytoplasm were evaluated with primers developed from the orfA501 sequence to distinguish between N- and T-cytoplasms. An amplicon with primers to the mitocondrial atp9 gene was used as an internal control. The two-step HRM marker system was tested using 246 onion plants. HRM analysis showed that the most common source of CMS, often used by Russian breeders, was S-cytoplasm; the rarest type of CMS was R-cytoplasm; and the proportion of T-cytoplasm among the analyzed breeding lines was 20.5%. The identification of the cytoplasm of a single plant by phenotype takes from 4 to 8 years. The HRM-based system enables quick and easy distinguishing of the four types of onion cytoplasm. Full article

(This article belongs to the Special Issue Genetics and Multi-Omics for Crop Breeding)

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17 pages, 4984 KiB

Open AccessArticle

Integrating Genetic and Chromosome Maps of Allium cepa: From Markers Visualization to Genome Assembly Verification

by Aleksey Ermolaev, Natalia Kudryavtseva, Anton Pivovarov, Ilya Kirov, Gennady Karlov and Ludmila Khrustaleva

Int. J. Mol. Sci. 2022, 23(18), 10486; https://doi.org/10.3390/ijms231810486 - 10 Sep 2022

Cited by 1 | Viewed by 1714

Abstract

The ability to directly look into genome sequences has opened great opportunities in plant breeding. Yet, the assembly of full-length chromosomes remains one of the most difficult problems in modern genomics. Genetic maps are commonly used in de novo genome assembly and are constructed on the basis of a statistical analysis of the number of recombinations. This may affect the accuracy of the ordering and orientation of scaffolds within the chromosome, especially in the region of recombination suppression. Moreover, it is impossible to assign contigs lacking DNA markers. Here, we report the use of Tyr-FISH to determine the position of the short DNA sequence of markers and non-mapped unique copy sequence on the physical chromosomes of a large-genome onion (Allium cepa L.). In order to minimize potential background masking of the target signal, we improved our earlier developed pipeline for probe design. A total of 23 markers were located on physical chromosomes 2 and 6. The order of markers was corrected by the integration of genetic, pseudochromosome maps and cytogenetic maps. Additionally, the position of the mlh1 gene, which was not on the genetic map, was defined on physical chromosome 2. Tyr-FISH mapping showed that the order of 23.1% (chromosome 2) and 27.3% (chromosome 6) of the tested genes differed between physical chromosomes and pseudochromosomes. The results can be used for the improvement of pseudochromosome 2 and 6 assembly. The present study aims to demonstrate the value of the in situ visualization of DNA sequences in chromosome-scaffold genome assembly. Full article

(This article belongs to the Special Issue Genetics and Multi-Omics for Crop Breeding)

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22 pages, 2609 KiB

Open AccessReview

Genome-Wide Datasets of Chicories (Cichorium intybus L.) for Marker-Assisted Crop Breeding Applications: A Systematic Review and Meta-Analysis

by Samela Draga, Giovanni Gabelli, Fabio Palumbo and Gianni Barcaccia

Int. J. Mol. Sci. 2023, 24(14), 11663; https://doi.org/10.3390/ijms241411663 - 19 Jul 2023

Cited by 1 | Viewed by 1171

Abstract

Cichorium intybus L. is the most economically important species of its genus and among the most important of the Asteraceae family. In chicory, many linkage maps have been produced, several sets of mapped and unmapped markers have been developed, and dozens of genes linked to traits of agronomic interest have been investigated. This treasure trove of information, properly cataloged and organized, is of pivotal importance for the development of superior commercial products with valuable agronomic potential in terms of yield and quality, including reduced bitter taste and increased inulin production, as well as resistance or tolerance to pathogens and resilience to environmental stresses. For this reason, a systematic review was conducted based on the scientific literature published in chicory during 1980–2023. Based on the results obtained from the meta-analysis, we created two consensus maps capable of supporting marker-assisted breeding (MAB) and marker-assisted selection (MAS) programs. By taking advantage of the recently released genome of C. intybus, we built a 639 molecular marker-based consensus map collecting all the available mapped and unmapped SNP and SSR loci available for this species. In the following section, after summarizing and discussing all the genes investigated in chicory and related to traits of interest such as reproductive barriers, sesquiterpene lactone biosynthesis, inulin metabolism and stress response, we produced a second map encompassing 64 loci that could be useful for MAS purposes. With the advent of omics technologies, molecular data chaos (namely, the situation where the amount of molecular data is so complex and unmanageable that their use becomes challenging) is becoming far from a negligible issue. In this review, we have therefore tried to contribute by standardizing and organizing the molecular data produced thus far in chicory to facilitate the work of breeders. Full article

(This article belongs to the Special Issue Genetics and Multi-Omics for Crop Breeding)

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