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Next-Generation Research on Plant Genetic Resources: Digital Phenotyping, Genomics, Phenomics and Phytochemicals

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Keywords
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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 9956

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Special Issue Editors

Dr. Seong-Hoon Kim

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Guest Editor

National Agrobiodiversity Center (Genebank), National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea
Interests: genebank; digital phenotyping; phytochemical; GWAS

Dr. Jung Bong Kim

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Guest Editor

Department of Agro-food Resources, National Institute of Agricultural Sciences, Rural Development Administration, 166, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, Republic of Korea
Interests: allium hookeri; linoleic acid; flavonols; polyunsaturated fatty acid; eicosapentaenoic acid

Dr. Inchan Choi

E-Mail Website
Guest Editor

Department of Agricultural Engineering, Rural Development Administration, National Institute of Agricultural Sciences, Jeonju, 54875, Republic of Korea
Interests: artificial Intelligence; phenomics; smart-farm; intelligence system; image detection

Special Issue Information

Dear Colleagues,

Major international plant gene banks such as ARS in the United States, IPK in Germany, VIR in Russia, NARO in Japan, and RDA-Genebank in Korea recognize the importance of plant genetic resources and are making every effort to collect, conserve, and evaluate plants. Due to anthropogenic activities, global warming and abnormal climate, the growing environment of crops is changing rapidly and we need new age crops that can adapt to the changing climate conditions. In this situation, genetic resources can be serve as excellent sources for breeding programs.
With the development of technology, the method of the phenotyping of crops is also becoming digital. In particular, the characterization of large quantities of resources conserved in genebanks can be done by applying digital techniques and applying high throughput phenotyping method.

This Special Issue on “Next-generation Research on Plant Genetic Resources: Digital phenotyping, Genomics, Phenomics and Phytochemicals” will cover a wide range of topics, including but not limited to from digital phenotyping to phytochemicals and genomics.

We warmly invite our colleagues to submit their original contributions to this Special Issue in order to provide recent updates regarding genebank, plant genetic resources and utilizaion that will be of interest to our readers. We would be delighted if you could respond to confirm your contribution and the proposed title to assist in planning the whole issue.

Dr. Seong-Hoon Kim
Dr. Jung Bong Kim
Dr. Inchan Choi
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. Plants is an international peer-reviewed open access semimonthly 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

genebank
germplasm
diversity
phytochemicals
secondary metabolites
natural products
digital phenotyping
GWAS

Published Papers (6 papers)

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Research

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25 pages, 2039 KiB

Open AccessArticle

Analysis of Genetic Diversity in Adzuki Beans (Vigna angularis): Insights into Environmental Adaptation and Early Breeding Strategies for Yield Improvement

by Xiaohan Wang, Yu-Mi Choi, Young-ah Jeon, JungYoon Yi, Myoung-Jae Shin, Kebede Taye Desta and Hyemyeong Yoon

Plants 2023, 12(24), 4154; https://doi.org/10.3390/plants12244154 - 13 Dec 2023

Viewed by 966

Abstract

Adzuki beans are widely cultivated in East Asia and are one of the earliest domesticated crops. In order to gain a deeper understanding of the genetic diversity and domestication history of adzuki beans, we conducted Genotyping by Sequencing (GBS) analysis on 366 landraces originating from Korea, China, and Japan, resulting in 6586 single-nucleotide polymorphisms (SNPs). Population structure analysis divided these 366 landraces into three subpopulations. These three subpopulations exhibited distinctive distributions, suggesting that they underwent extended domestication processes in their respective regions of origin. Phenotypic variance analysis of the three subpopulations indicated that the Korean-domesticated subpopulation exhibited significantly higher 100-seed weights, the Japanese-domesticated subpopulation showed significantly higher numbers of grains per pod, and the Chinese-domesticated subpopulation displayed significantly higher numbers of pods per plant. We speculate that these differences in yield-related traits may be attributed to varying emphases placed by early breeders in these regions on the selection of traits related to yield. A large number of genes related to biotic/abiotic stress resistance and defense were found in most quantitative trait locus (QTL) for yield-related traits using genome-wide association studies (GWAS). Genomic sliding window analysis of Tajima’s D and a genetic differentiation coefficient (Fst) revealed distinct domestication selection signatures and genotype variations on these QTLs within each subpopulation. These findings indicate that each subpopulation would have been subjected to varied biotic/abiotic stress events in different origins, of which these stress events have caused balancing selection differences in the QTL of each subpopulation. In these balancing selections, plants tend to select genotypes with strong resistance under biotic/abiotic stress, but reduce the frequency of high-yield genotypes to varying degrees. These biotic/abiotic stressors impact crop yield and may even lead to selection purging, resulting in the loss of several high-yielding genotypes among landraces. However, this also fuels the flow of crop germplasms. Overall, balancing selection appears to have a more significant impact on the three yield-related traits compared to breeder-driven domestication selection. These findings are crucial for understanding the impact of domestication selection history on landraces and yield-related traits, aiding in the improvement of adzuki bean varieties. Full article

(This article belongs to the Special Issue Next-Generation Research on Plant Genetic Resources: Digital Phenotyping, Genomics, Phenomics and Phytochemicals)

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10 pages, 2001 KiB

Open AccessCommunication

Automatic Evaluation of Soybean Seed Traits Using RGB Image Data and a Python Algorithm

by Amit Ghimire, Seong-Hoon Kim, Areum Cho, Naeun Jang, Seonhwa Ahn, Mohammad Shafiqul Islam, Sheikh Mansoor, Yong Suk Chung and Yoonha Kim

Plants 2023, 12(17), 3078; https://doi.org/10.3390/plants12173078 - 28 Aug 2023

Cited by 3 | Viewed by 1262

Abstract

Soybean (Glycine max) is a crucial legume crop known for its nutritional value, as its seeds provide large amounts of plant protein and oil. To ensure maximum productivity in soybean farming, it is essential to carefully choose high-quality seeds that possess desirable characteristics, such as the appropriate size, shape, color, and absence of any damage. By studying the relationship between seed shape and other traits, we can effectively identify different genotypes and improve breeding strategies to develop high-yielding soybean seeds. This study focused on the analysis of seed traits using a Python algorithm. The seed length, width, projected area, and aspect ratio were measured, and the total number of seeds was calculated. The OpenCV library along with the contour detection function were used to measure the seed traits. The seed traits obtained through the algorithm were compared with the values obtained manually and from two software applications (SmartGrain and WinDIAS). The algorithm-derived measurements for the seed length, width, and projected area showed a strong correlation with the measurements obtained using various methods, with R-square values greater than 0.95 (p < 0.0001). Similarly, the error metrics, including the residual standard error, root mean square error, and mean absolute error, were all below 0.5% when comparing the seed length, width, and aspect ratio across different measurement methods. For the projected area, the error was less than 4% when compared with different measurement methods. Furthermore, the algorithm used to count the number of seeds present in the acquired images was highly accurate, and only a few errors were observed. This was a preliminary study that investigated only some morphological traits, and further research is needed to explore more seed attributes. Full article

(This article belongs to the Special Issue Next-Generation Research on Plant Genetic Resources: Digital Phenotyping, Genomics, Phenomics and Phytochemicals)

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11 pages, 2985 KiB

Open AccessFeature PaperArticle

RDA-Genebank and Digital Phenotyping for Next-Generation Research on Plant Genetic Resources

by Seong-Hoon Kim, Parthiban Subramanian, Young-Wang Na, Bum-Soo Hahn and Yoonha Kim

Plants 2023, 12(15), 2825; https://doi.org/10.3390/plants12152825 - 31 Jul 2023

Viewed by 1009

Abstract

The National Agrobiodiversity Center under the Rural Development Administration (RDA) in Jeonju, Republic of Korea stands as the foremost national genebank in the country. Over the years, the National Agrobiodiversity Center has remained committed to enriching its collection with foreign genetic resources, elevating its status to a world-class plant genetic resources (PGR)- holding genebank. Currently, several steps are being undertaken to improve the accessibility of the collection to national as well as international researchers, improve the data available on the resources, and amend the passport information for the accessions. With the implementation of the Nagoya Protocol, the origin of genetic resources is being highlighted as an important input in the passport information. The RDA-Genebank actively responds to the Nagoya Protocol by supplementing passport data for resources lacking information on their origin. In addition, a large number of conserved resources are continuously multiplied, and agronomic traits are investigated concurrently. With the traditional methods of characterization of the germplasm requiring a significant amount of time and effort, we have initiated high-throughput phenotyping using digital techniques to improve our germplasm data. Primarily, we have started adding seed phenotype information followed by measuring root phenotypes which are stored under agronomic traits. This may be the initial step toward using largescale high-throughput techniques for a germplasm. In this study, we aim to provide an introduction to the RDA-Genebank, to adopted international standards, and to the establishment of high-throughput phenotyping techniques for the improvement of passport information. Full article

(This article belongs to the Special Issue Next-Generation Research on Plant Genetic Resources: Digital Phenotyping, Genomics, Phenomics and Phytochemicals)

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15 pages, 2696 KiB

Open AccessArticle

Investigation of the Relationship between Genetic and Breeding Characteristics of WBPH Behavior according to Resistant Materials in Rice

by Jae-Ryoung Park, Eun-Gyeong Kim, Yoon-Hee Jang, Sang Yong Nam and Kyung-Min Kim

Plants 2023, 12(15), 2821; https://doi.org/10.3390/plants12152821 - 30 Jul 2023

Viewed by 858

Abstract

Rice accounts for most of the calories consumed by the world’s population. However, the whitebacked planthopper (WBPH), Sogatella furcifera (Horvath), is an insect that can cause rice yield loss. WBPH sucks the stems of rice and negatively affects yield and grain quality. Therefore, numerous insecticides have been developed to control WBPH in rice fields. However, chemical pesticides cause serious problems such as environmental pollution and ecosystem disturbance. Here, we research the possibility of using previously reported rice extracts obtained using methanol, Chrysoeriol 7(C7) and Cochlioquinone-9 (cq-9), as potential insect repellents. WBPH was caged with C7 or cq-9 and monitored, and the WBPH behavior was recorded. The number of WBPHs approaching the periphery of the C7 and cq-9 was very low. In cages containing the C7 and cq-9, only 13 and 7 WBPHs out of 100, respectively, walked around the material. In addition, foliar spraying with C7 and cq-9 did not negatively affect the plant height. The expression level of genes related to resistance was maintained at a high level in the resistant lines when treated with WBPHs alone, but was at a similar level to those of the controls when treated with C7 or cq-9. Interfering with WBPH access did not adversely affect the plant phenotype. Recently, people’s interest in the environment has increased, and the use of plant-derived materials is also increasing. There is a new trend towards using plant extracts as an environmentally friendly means of managing resistance to WBPH during the rice cultivation period, while also avoiding environmental pollution. Full article

(This article belongs to the Special Issue Next-Generation Research on Plant Genetic Resources: Digital Phenotyping, Genomics, Phenomics and Phytochemicals)

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14 pages, 3393 KiB

Open AccessArticle

A Genome-Wide Association Study of Protein, Oil, and Amino Acid Content in Wild Soybean (Glycine soja)

by Woon Ji Kim, Byeong Hee Kang, Sehee Kang, Seoyoung Shin, Sreeparna Chowdhury, Soon-Chun Jeong, Man-Soo Choi, Soo-Kwon Park, Jung-Kyung Moon, Jaihyunk Ryu and Bo-Keun Ha

Plants 2023, 12(8), 1665; https://doi.org/10.3390/plants12081665 - 16 Apr 2023

Cited by 2 | Viewed by 1873

Abstract

Soybean (Glycine max L.) is a globally important source of plant proteins, oils, and amino acids for both humans and livestock. Wild soybean (Glycine soja Sieb. and Zucc.), the ancestor of cultivated soybean, could be a useful genetic source for increasing these components in soybean crops. In this study, 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom^® Soya SNP array were investigated using an association analysis. Protein and oil content exhibited a highly significant negative correlation, while the 17 amino acids exhibited a highly significant positive correlation with each other. A genome-wide association study (GWAS) was conducted on the protein, oil, and amino acid content using the 203 wild soybean accessions. A total of 44 significant SNPs were associated with protein, oil, and amino acid content. Glyma.11g015500 and Glyma.20g050300, which contained SNPs detected from the GWAS, were selected as novel candidate genes for the protein and oil content, respectively. In addition, Glyma.01g053200 and Glyma.03g239700 were selected as novel candidate genes for nine of the amino acids (Ala, Asp, Glu, Gly, Leu, Lys, Pro, Ser, and Thr). The identification of the SNP markers related to protein, oil, and amino acid content reported in the present study is expected to help improve the quality of selective breeding programs for soybeans. Full article

(This article belongs to the Special Issue Next-Generation Research on Plant Genetic Resources: Digital Phenotyping, Genomics, Phenomics and Phytochemicals)

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Review

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19 pages, 637 KiB

Open AccessReview

Conservation and Global Distribution of Onion (Allium cepa L.) Germplasm for Agricultural Sustainability

by Kingsley Ochar and Seong-Hoon Kim

Plants 2023, 12(18), 3294; https://doi.org/10.3390/plants12183294 - 18 Sep 2023

Cited by 2 | Viewed by 3098

Abstract

Onion (Allium cepa L.) is recognized globally as a crucial vegetable crop, prized not only for its culinary applications but also for its numerous health-promoting properties. With climate change relentlessly exerting mounting challenges to agriculture, the preservation and deployment of onion germplasm has become critical to ensuring sustainable agriculture and safeguarding food security. Global onion germplasm collections function as repositories of genetic diversity, holding within them an extensive array of valuable traits or genes. These can be harnessed to develop varieties resilient to climate adversities. Therefore, detailed information concerning onion germplasm collections from various geographical regions can bolster their utility. Furthermore, an amplified understanding of the importance of fostering international and inter-institutional collaborations becomes essential. Sharing and making use of onion genetic resources can provide viable solutions to the looming agricultural challenges of the future. In this review, we have discussed the preservation and worldwide distribution of onion germplasm, along with its implications for agricultural sustainability. We have also underscored the importance of international and interinstitutional collaboration in onion germplasm collecting and conservation for agricultural sustainability. Full article

(This article belongs to the Special Issue Next-Generation Research on Plant Genetic Resources: Digital Phenotyping, Genomics, Phenomics and Phytochemicals)

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