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Identification and Application of Natural Genetic Resources for Plant Improvement
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Identification and Application of Natural Genetic Resources for Plant Improvement

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 (30 April 2021) | Viewed by 11581

Special Issue Editor

Prof. Dr. Byeong-ha Lee

E-Mail Website
Guest Editor
Department of Life Science, Sogang University, Seoul 04107, Republic of Korea
Interests: plant abiotic stress tolerance; plant development; RNA processing and regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Maybe the most fascinating thing in biology is diversity. Without diversity, we would not expect evolution. Throughout evolutionary history, plants developed various survival strategies in their metabolisms, developments, and defenses to environmental constraints. This means that many plants might have elite or superior gene alleles that show more favorable traits than others. Mining of these superior alleles becomes important when it comes to modern crops. Modern crop domestication favored crop yield over the other traits such as stress tolerance. Thus, many such traits have been lost in modern crops. Now the global climate issues and the world food crisis make us look another direction – we need to re-introduce the lost traits to improve plants and crops. With the accumulated knowledge of gene functions and the current biotechniques such as gene editing tools, we could control the yield penalty that we might need to pay by introducing lost or new traits. The first step is to find natural genetic resources from crop progenitors, natural variants, and extremophiles.

This Special Issue is designed to help discussions in natural genetic resources for plant improvements, and accepts reviews and research articles that covers the identification and use of elite alleles preferably in a comparative study.

Prof. Dr. Byeong-ha Lee
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • natural variations
  • superior alleles
  • elite alleles
  • accessions
  • ecotypes
  • wild progenitors
  • crop progenitors
  • crop improvements

Published Papers (4 papers)

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Research

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20 pages, 5093 KiB  
Article
Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing
by Do Yoon Hyun, Raveendar Sebastin, Gi-An Lee, Kyung Jun Lee, Seong-Hoon Kim, Eunae Yoo, Sookyeong Lee, Man-Jung Kang, Seung Bum Lee, Ik Jang, Na-Young Ro and Gyu-Taek Cho
Int. J. Mol. Sci. 2021, 22(13), 6722; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22136722 - 23 Jun 2021
Cited by 9 | Viewed by 3209
Abstract
Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon ( [...] Read more.
Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank. Full article
(This article belongs to the Special Issue Identification and Application of Natural Genetic Resources for Plant Improvement)
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19 pages, 2347 KiB  
Article
Quantitative Control of Early Flowering in White Lupin (Lupinus albus L.)
by Sandra Rychel-Bielska, Anna Surma, Wojciech Bielski, Bartosz Kozak, Renata Galek and Michał Książkiewicz
Int. J. Mol. Sci. 2021, 22(8), 3856; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22083856 - 08 Apr 2021
Cited by 5 | Viewed by 2365
Abstract
White lupin (Lupinus albus L.) is a pulse annual plant cultivated from the tropics to temperate regions for its high-protein grain as well as a cover crop or green manure. Wild populations are typically late flowering and have high vernalization requirements. Nevertheless, [...] Read more.
White lupin (Lupinus albus L.) is a pulse annual plant cultivated from the tropics to temperate regions for its high-protein grain as well as a cover crop or green manure. Wild populations are typically late flowering and have high vernalization requirements. Nevertheless, some early flowering and thermoneutral accessions were found in the Mediterranean basin. Recently, quantitative trait loci (QTLs) explaining flowering time variance were identified in bi-parental population mapping, however, phenotypic and genotypic diversity in the world collection has not been addressed yet. In this study, a diverse set of white lupin accessions (n = 160) was phenotyped for time to flowering in a controlled environment and genotyped with PCR-based markers (n = 50) tagging major QTLs and selected homologs of photoperiod and vernalization pathway genes. This survey highlighted quantitative control of flowering time in white lupin, providing statistically significant associations for all major QTLs and numerous regulatory genes, including white lupin homologs of CONSTANS, FLOWERING LOCUS T, FY, MOTHER OF FT AND TFL1, PHYTOCHROME INTERACTING FACTOR 4, SKI-INTERACTING PROTEIN 1, and VERNALIZATION INDEPENDENCE 3. This revealed the complexity of flowering control in white lupin, dispersed among numerous loci localized on several chromosomes, provided economic justification for future genome-wide association studies or genomic selection rather than relying on simple marker-assisted selection. Full article
(This article belongs to the Special Issue Identification and Application of Natural Genetic Resources for Plant Improvement)
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20 pages, 3500 KiB  
Article
A Novel Protein from Ectocarpus sp. Improves Salinity and High Temperature Stress Tolerance in Arabidopsis thaliana
by Pramod Rathor, Tudor Borza, Sophia Stone, Thierry Tonon, Svetlana Yurgel, Philippe Potin and Balakrishnan Prithiviraj
Int. J. Mol. Sci. 2021, 22(4), 1971; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041971 - 17 Feb 2021
Cited by 4 | Viewed by 2537
Abstract
Brown alga Ectocarpus sp. belongs to Phaeophyceae, a class of macroalgae that evolved complex multicellularity. Ectocarpus sp. is a dominant seaweed in temperate regions, abundant mostly in the intertidal zones, an environment with high levels of abiotic stresses. Previous transcriptomic analysis of Ectocarpus [...] Read more.
Brown alga Ectocarpus sp. belongs to Phaeophyceae, a class of macroalgae that evolved complex multicellularity. Ectocarpus sp. is a dominant seaweed in temperate regions, abundant mostly in the intertidal zones, an environment with high levels of abiotic stresses. Previous transcriptomic analysis of Ectocarpus sp. revealed several genes consistently induced by various abiotic stresses; one of these genes is Esi0017_0056, which encodes a protein with unknown function. Bioinformatics analyses indicated that the protein encoded by Esi0017_0056 is soluble and monomeric. The protein was successfully expressed in Escherichia coli,Arabidopsis thaliana and Nicotiana benthamiana. In A. thaliana the gene was expressed under constitutive and stress inducible promoters which led to improved tolerance to high salinity and temperature stresses. The expression of several key abiotic stress-related genes was studied in transgenic and wild type A. thaliana by qPCR. Expression analysis revealed that genes involved in ABA-induced abiotic stress tolerance, K+ homeostasis, and chaperon activities were significantly up-regulated in the transgenic line. This study is the first report in which an unknown function Ectocarpus sp. gene, highly responsive to abiotic stresses, was successfully expressed in A. thaliana, leading to improved tolerance to salt and temperature stress. Full article
(This article belongs to the Special Issue Identification and Application of Natural Genetic Resources for Plant Improvement)
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Review

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15 pages, 315 KiB  
Review
Natural Genetic Resources from Diverse Plants to Improve Abiotic Stress Tolerance in Plants
by Seher Yolcu, Hemasundar Alavilli and Byeong-ha Lee
Int. J. Mol. Sci. 2020, 21(22), 8567; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21228567 - 13 Nov 2020
Cited by 20 | Viewed by 2636
Abstract
The current agricultural system is biased for the yield increase at the cost of biodiversity. However, due to the loss of precious genetic diversity during domestication and artificial selection, modern cultivars have lost the adaptability to cope with unfavorable environments. There are many [...] Read more.
The current agricultural system is biased for the yield increase at the cost of biodiversity. However, due to the loss of precious genetic diversity during domestication and artificial selection, modern cultivars have lost the adaptability to cope with unfavorable environments. There are many reports on variations such as single nucleotide polymorphisms (SNPs) and indels in the stress-tolerant gene alleles that are associated with higher stress tolerance in wild progenitors, natural accessions, and extremophiles in comparison with domesticated crops or model plants. Therefore, to gain a better understanding of stress-tolerant traits in naturally stress-resistant plants, more comparative studies between the modern crops/model plants and crop progenitors/natural accessions/extremophiles are required. In this review, we discussed and summarized recent progress on natural variations associated with enhanced abiotic stress tolerance in various plants. By applying the recent biotechniques such as the CRISPR/Cas9 gene editing tool, natural genetic resources (i.e., stress-tolerant gene alleles) from diverse plants could be introduced to the modern crop in a non-genetically modified way to improve stress-tolerant traits. Full article
(This article belongs to the Special Issue Identification and Application of Natural Genetic Resources for Plant Improvement)
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