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A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics

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

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 36707

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Special Issue Editors

Prof. Dr. Petr Smýkal

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Department of Botany, Palacky University, 771 47 Olomouc, Czech Republic
Interests: domestication; crop wild relatives; genetic diversity; legumes; seed dormancy; seed dispersal
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Eric Von Wettberg

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Guest Editor

Department of Plant and Soil Science and Gund Institute for the Environment, University of Vermont, Burlington, VT 05405, USA
Interests: domestication; legumes; local adaptation; crop rotations; abiotic stress tolerance; soil carbon

Dr. Giovanni Malerba

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Guest Editor

GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
Interests: genomics and transcriptomics of Mendelian and complex traits; association and Linkage analyses; statistical genetics and bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue celebrates the bicentennial of the birth of Gregor Johann Mendel, the genius of genetics.

Gregor Johann Mendel has left an indelible mark on the history of science. His work, together with Darwin’s evolutionary theory, established the theoretical basis of today’s biology. Many books and reviews have been written about his life and scientific achievements, and Mendel’s principles of heredity now belong to general education and are found in every biology textbook.

Essentially every paper involving genetic study is celebration of his work. It also impacts our everyday lives—including our health but also medicine, agriculture and conservation. The rules found by Mendel remain valid forever.

His genius originated from the use of several novel approaches, until his time not commonly used in biology, such as use of mathematical and statistical analysis. This allowed him to formulate general conclusions on hereditary rules, based on exact experiments.

Biological sciences are increasingly a collaborative domain, with research projects including aspects of physics, mathematics and chemistry. This is fueled by the technical advances such as DNA sequencing, allowing for more discoveries, but also creating new challenges, such as data storage, analysis and predictions. This led to the establishment of systems biology, as an integrative approach to understand complex networks that characterize the phenotypes in the cell that draws techniques and approaches from multiple disciplines.

Mendel’s bicentenary provides a great opportunity for presenting recent developments and the latest research in the wide fascinating broad range of today´s biology—plants, animals and microbial kingdoms, from evolutionary to modern breeding approaches.

Prof. Dr. Petr Smýkal
Prof. Dr. Eric Von Wettberg
Dr. Giovanni Malerba
Guest Editors

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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

breeding
evolution
genetics
genomics
Gregor Mendel
heredity
hybridization
variation

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Published Papers (9 papers)

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Editorial

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4 pages, 217 KiB

Open AccessEditorial

A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics

by Petr Smýkal and Eric J. B. von Wettberg

Int. J. Mol. Sci. 2023, 24(14), 11718; https://doi.org/10.3390/ijms241411718 - 20 Jul 2023

Viewed by 1281

Abstract

In celebration of the bicentennial of the birth of Gregor Johann Mendel, the genius of genetics, this Special Issue presents seven papers [...] Full article

(This article belongs to the Special Issue A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics)

Research

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13 pages, 3643 KiB

Open AccessArticle

Genome-Wide Detection of Quantitative Trait Loci and Prediction of Candidate Genes for Seed Sugar Composition in Early Mature Soybean

by Li Hu, Xianzhi Wang, Jiaoping Zhang, Liliana Florez-Palacios, Qijian Song and Guo-Liang Jiang

Int. J. Mol. Sci. 2023, 24(4), 3167; https://doi.org/10.3390/ijms24043167 - 5 Feb 2023

Cited by 4 | Viewed by 1998

Abstract

Seed sugar composition, mainly including fructose, glucose, sucrose, raffinose, and stachyose, is an important indicator of soybean [Glycine max (L.) Merr.] seed quality. However, research on soybean sugar composition is limited. To better understand the genetic architecture underlying the sugar composition in soybean seeds, we conducted a genome-wide association study (GWAS) using a population of 323 soybean germplasm accessions which were grown and evaluated under three different environments. A total of 31,245 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) ≥ 5% and missing data ≤ 10% were selected and used in the GWAS. The analysis identified 72 quantitative trait loci (QTLs) associated with individual sugars and 14 with total sugar. Ten candidate genes within the 100 Kb flanking regions of the lead SNPs across six chromosomes were significantly associated with sugar contents. According to GO and KEGG classification, eight genes were involved in the sugar metabolism in soybean and showed similar functions in Arabidopsis. The other two, located in known QTL regions associated with sugar composition, may play a role in sugar metabolism in soybean. This study advances our understanding of the genetic basis of soybean sugar composition and facilitates the identification of genes controlling this trait. The identified candidate genes will help improve seed sugar composition in soybean. Full article

(This article belongs to the Special Issue A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics)

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19 pages, 2959 KiB

Open AccessArticle

Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection

by Nicolas Rispail, Osman Zakaria Wohor, Salvador Osuna-Caballero, Eleonora Barilli and Diego Rubiales

Int. J. Mol. Sci. 2023, 24(3), 2470; https://doi.org/10.3390/ijms24032470 - 27 Jan 2023

Cited by 14 | Viewed by 3470

Abstract

Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD₅₀ distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of Pisum genus into two species, P. fulvum and P. sativum (including subsp. sativum, arvense, elatius, humile, jomardii and abyssinicum). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate P. sativum subsp. jomardii and P. sativum subsp. arvense during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches. Full article

(This article belongs to the Special Issue A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics)

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19 pages, 2300 KiB

Open AccessArticle

Lifestage Sex-Specific Genetic Effects on Metabolic Disorders in an Adult Population in Korea: The Korean Genome and Epidemiology Study

by Young-Sang Kim, Yon Chul Park, Ja-Eun Choi, Jae-Min Park, Kunhee Han, Kwangyoon Kim, Bom-Taeck Kim and Kyung-Won Hong

Int. J. Mol. Sci. 2022, 23(19), 11889; https://doi.org/10.3390/ijms231911889 - 6 Oct 2022

Cited by 2 | Viewed by 14795

Abstract

Although many genome-wide association studies (GWASs) have evaluated the association with metabolic disorders, the current study is the first attempt to analyze the genetic risk factors for various metabolic disorders according to sex and age groups of the life course in Korean adults. A total population of 50,808 people were included in this GWAS. The genetic traits for eight metabolic phenotypes were investigated in peri-, and postmenopausal women compared to a younger group or men of corresponding age groups. The metabolic phenotypes include general obesity, abdominal obesity, hypertension, type 2 diabetes, hypercholesterolemia, hypertriglyceridemia, hypo-high-density lipoprotein cholesterolemia, and metabolic syndrome. In the total participants, GWAS results for eight metabolic phenotypes found 101 significant loci. Of these, 15 loci were the first reported to be associated with the risk of metabolic disorder. Interestingly, some of the significant loci presented the association with the various phenotypes, which presented when there was a correlation between phenotypes. In addition, we analyzed divided by gender and age (young adult, peri-menopausal group, older adult), and specifically identified specific loci in peri-menopausal women. Meanwhile, several genetic factors associated with metabolic disorders were newly reported in our study. In particular, several genes were significantly associated with one of the metabolic phenotypes in only a single specific group. These findings suggest that menopausal transition rather than aging itself potentiates the influence of genetic risks on metabolic disorders. In addition, some genetic loci with low frequencies may play a role in the metabolic disturbances in a specific sex and age group. The genetic traits derived from our study may contribute to understanding the genetic risk factors for metabolic disorders in the Korean population. Full article

(This article belongs to the Special Issue A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics)

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16 pages, 5088 KiB

Open AccessArticle

Disease Resistance and Molecular Variations in Irradiation Induced Mutants of Two Pea Cultivars

by Dong Deng, Suli Sun, Wenqi Wu, Chao Xiang, Canxing Duan, Dongmei Yu, Xuehong Wu and Zhendong Zhu

Int. J. Mol. Sci. 2022, 23(15), 8793; https://doi.org/10.3390/ijms23158793 - 8 Aug 2022

Cited by 4 | Viewed by 1801

Abstract

Induced mutation is useful for improving the disease resistance of various crops. Fusarium wilt and powdery mildew are two important diseases which severely influence pea production worldwide. In this study, we first evaluated Fusarium wilt and powdery mildew resistance of mutants derived from two elite vegetable pea cultivars, Shijiadacaiwan 1 (SJ1) and Chengwan 8 (CW8), respectively. Nine SJ1 and five CW8 M₃ mutants showed resistant variations in Fusarium wilt, and the same five CW8 mutants in powdery mildew. These resistant variations were confirmed in M₄ and M₅ mutants as well. Then, we investigated the genetic variations and relationships of mutant lines using simple sequence repeat (SSR) markers. Among the nine effective SSR markers, the genetic diversity index and polymorphism information content (PIC) values were averaged at 0.55 and 0.46, which revealed considerable genetic variations in the mutants. The phylogenetic tree and population structure analyses divided the M₃ mutants into two major groups at 0.62 genetic similarity (K = 2), which clearly separated the mutants of the two cultivars and indicated that a great genetic difference existed between the two mutant populations. Further, the two genetic groups were divided into five subgroups at 0.86 genetic similarity (K = 5) and each subgroup associated with resistant phenotypes of the mutants. Finally, the homologous PsMLO1 cDNA of five CW8 mutants that gained resistance to powdery mildew was amplified and cloned. A 129 bp fragment deletion was found in the PsMLO1 gene, which was in accord with er1-2. The findings provide important information on disease resistant and molecular variations of pea mutants, which is useful for pea production, new cultivar breeding, and the identification of resistance genes. Full article

(This article belongs to the Special Issue A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics)

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12 pages, 1995 KiB

Open AccessArticle

The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences—Implications for Evolution and Biological Regulation

by Michaela Dobrovolná, Natália Bohálová, Vratislav Peška, Jiawei Wang, Yu Luo, Martin Bartas, Adriana Volná, Jean-Louis Mergny and Václav Brázda

Int. J. Mol. Sci. 2022, 23(15), 8482; https://doi.org/10.3390/ijms23158482 - 30 Jul 2022

Cited by 9 | Viewed by 2236

Abstract

G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5′UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome. Full article

(This article belongs to the Special Issue A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics)

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Review

Jump to: Editorial, Research

24 pages, 2865 KiB

Open AccessReview

Genomic Instability Evolutionary Footprints on Human Health: Driving Forces or Side Effects?

by Laura Veschetti, Mirko Treccani, Elisa De Tomi and Giovanni Malerba

Int. J. Mol. Sci. 2023, 24(14), 11437; https://doi.org/10.3390/ijms241411437 - 14 Jul 2023

Cited by 4 | Viewed by 2452

Abstract

In this work, we propose a comprehensive perspective on genomic instability comprising not only the accumulation of mutations but also telomeric shortening, epigenetic alterations and other mechanisms that could contribute to genomic information conservation or corruption. First, we present mechanisms playing a role in genomic instability across the kingdoms of life. Then, we explore the impact of genomic instability on the human being across its evolutionary history and on present-day human health, with a particular focus on aging and complex disorders. Finally, we discuss the role of non-coding RNAs, highlighting future approaches for a better living and an expanded healthy lifespan. Full article

(This article belongs to the Special Issue A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics)

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16 pages, 646 KiB

Open AccessReview

Spontaneous, Artificial, and Genome Editing-Mediated Mutations in Prunus

by Angel S. Prudencio, Sama Rahimi Devin, Sayyed Mohammad Ehsan Mahdavi, Pedro J. Martínez-García, Juan A. Salazar and Pedro Martínez-Gómez

Int. J. Mol. Sci. 2022, 23(21), 13273; https://doi.org/10.3390/ijms232113273 - 31 Oct 2022

Cited by 8 | Viewed by 3300

Abstract

Mutation is a source of genetic diversity widely used in breeding programs for the acquisition of agronomically interesting characters in commercial varieties of the Prunus species, as well as in the rest of crop species. Mutation can occur in nature at a very low frequency or can be induced artificially. Spontaneous or bud sport mutations in somatic cells can be vegetatively propagated to get an individual with the mutant phenotype. Unlike animals, plants have unlimited growth and totipotent cells that let somatic mutations to be transmitted to the progeny. On the other hand, in vitro tissue culture makes it possible to induce mutation in plant material and perform large screenings for mutant’s selection and cleaning of chimeras. Finally, targeted mutagenesis has been boosted by the application of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 and Transcription activator-like effector nuclease (TALEN) editing technologies. Over the last few decades, environmental stressors such as global warming have been threatening the supply of global demand for food based on population growth in the near future. For this purpose, the release of new varieties adapted to such changes is a requisite, and selected or generated Prunus mutants by properly regulated mechanisms could be helpful to this task. In this work, we reviewed the most relevant mutations for breeding traits in Prunus species such as flowering time, self-compatibility, fruit quality, and disease tolerance, including new molecular perspectives in the present postgenomic era including CRISPR/Cas9 and TALEN editing technologies. Full article

(This article belongs to the Special Issue A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics)

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14 pages, 738 KiB

Open AccessReview

Mechanisms of Vernalization-Induced Flowering in Legumes

by Svetlana Yu. Surkova and Maria G. Samsonova

Int. J. Mol. Sci. 2022, 23(17), 9889; https://doi.org/10.3390/ijms23179889 - 31 Aug 2022

Cited by 10 | Viewed by 3228

Abstract

Vernalization is the requirement for exposure to low temperatures to trigger flowering. The best knowledge about the mechanisms of vernalization response has been accumulated for Arabidopsis and cereals. In Arabidopsis thaliana, vernalization involves an epigenetic silencing of the MADS-box gene FLOWERING LOCUS C (FLC), which is a flowering repressor. FLC silencing releases the expression of the main flowering inductor FLOWERING LOCUS T (FT), resulting in a floral transition. Remarkably, no FLC homologues have been identified in the vernalization-responsive legumes, and the mechanisms of cold-mediated transition to flowering in these species remain elusive. Nevertheless, legume FT genes have been shown to retain the function of the main vernalization signal integrators. Unlike Arabidopsis, legumes have three subclades of FT genes, which demonstrate distinct patterns of regulation with respect to environmental cues and tissue specificity. This implies complex mechanisms of vernalization signal propagation in the flowering network, that remain largely elusive. Here, for the first time, we summarize the available information on the genetic basis of cold-induced flowering in legumes with a special focus on the role of FT genes. Full article

(This article belongs to the Special Issue A Commemorative Issue in Honor of 200th Anniversary of the Birth of Gregor Johann Mendel: The Genius of Genetics)

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