Plants

Editorial

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3 pages, 153 KiB

Open AccessEditorial

Advancing Plant Breeding with Next-Generation Technologies: Insights from Recent Research

by Seong-Hoon Kim, Inchan Choi and Jung-Bong Kim

Plants 2024, 13(20), 2877; https://doi.org/10.3390/plants13202877 - 15 Oct 2024

Viewed by 2381

Abstract

Genetic resources are the cornerstone of our food supply and play a pivotal role in developing new crop varieties that ensure sustainable agricultural production amid the challenges of climate change [...] Full article

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

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

Cited by 2 | Viewed by 2358

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 [...] Read more.

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 9 | Viewed by 2601

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 [...] Read more.

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

Cited by 3 | Viewed by 1694

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 [...] Read more.

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

Cited by 2 | Viewed by 1463

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, [...] Read more.

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 15 | Viewed by 4146

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 [...] Read more.

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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30 pages, 1368 KiB

Open AccessReview

Harnessing Single-Cell and Spatial Transcriptomics for Crop Improvement

by Yuzhao Hu, Linkan Dash, Gregory May, Nagesh Sardesai and Stéphane Deschamps

Plants 2024, 13(24), 3476; https://doi.org/10.3390/plants13243476 - 11 Dec 2024

Viewed by 1907

Abstract

Single-cell and spatial transcriptomics technologies have significantly advanced our understanding of the molecular mechanisms underlying crop biology. This review presents an update on the application of these technologies in crop improvement. The heterogeneity of different cell populations within a tissue plays a crucial [...] Read more.

Single-cell and spatial transcriptomics technologies have significantly advanced our understanding of the molecular mechanisms underlying crop biology. This review presents an update on the application of these technologies in crop improvement. The heterogeneity of different cell populations within a tissue plays a crucial role in the coordinated response of an organism to its environment. Single-cell transcriptomics enables the dissection of this heterogeneity, offering insights into the cell-specific transcriptomic responses of plants to various environmental stimuli. Spatial transcriptomics technologies complement single-cell approaches by preserving the spatial context of gene expression profiles, allowing for the in situ localization of transcripts. Together, single-cell and spatial transcriptomics facilitate the discovery of novel genes and gene regulatory networks that can be targeted for genetic manipulation and breeding strategies aimed at enhancing crop yield, quality, and resilience. This review highlights significant findings from recent studies, discusses the expanding roles of these technologies, and explores future opportunities for their application in crop improvement. 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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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 19 | Viewed by 10238

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 [...] Read more.

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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